Electronmicroscopy of genetic activity

Coordinated Control of rRNA Processing by RNA Polymerase I

Ribosomal RNA (rRNA) is co- and post-transcriptionally processed into active ribosomes. This process is dynamically regulated by direct covalent modifications of the polymerase that synthesizes the rRNA, RNA polymerase I (Pol I), and by interactions with cofactors that influence initiation, elongation, and termination activities of Pol I. The rate of transcription elongation by Pol I directly influences processing of nascent rRNA, and changes in Pol I transcription rate result in alternative rRNA processing events that lead to cellular signaling alterations and stress. It is clear that in divergent species, there exists robust organization of nascent rRNA processing events during transcription elongation. This review evaluates the current state of our understanding of the complex relationship between transcription elongation and rRNA processing.

The Fork in the Road: Histone Partitioning During DNA Replication

In the following discussion the distribution of histones at the replication fork is examined, with specific attention paid to the question of H3/H4 tetramer "splitting." After a presentation of early experiments surrounding this topic, more recent contributions are detailed. The implications of these findings with respect to the transmission of histone modifications and epigenetic models are also addressed.

Are lampbrush chromosomes unique to meiotic cells?

Lampbrush chromosomes (LBCs) are transcriptionally active chromosomes found in the germinal vesicle (GV) of large oocytes of many vertebrate and invertebrate animals and also in the giant single-celled alga Acetabularia. These cells are all in prophase of the first meiotic division. Nevertheless, many meiotic cells do not develop LBCs, arguing that LBCs are not an essential feature of meiosis. LBCs probably represent the most active transcriptional state that can be attained by cells that must give rise to diploid progeny. Polyploidy permits cells to reach higher rates of transcription per nucleus but precludes a return to diploidy. In this sense, LBCs represent a relatively inefficient transcriptional compromise employed by large meiotic cells. These considerations help to explain why transcriptionally active GVs develop LBCs, but they do not explain why LBCs have never been seen in somatic cells, diploid or otherwise. If LBCs are truly limited to germ cells, then some of their unusual features may reflect reprogramming of the genome. If this is the case, LBCs provide unique opportunities to study reprogramming at the level of the individual transcription unit.

Superresolution imaging of transcription units on newt lampbrush chromosomes

We have examined transcription loops on lampbrush chromosomes of the newt Notophthalmus by superresolution microscopy. Because of the favorable, essentially two-dimensional morphology of these loops, an average optical resolution in the x-y plane of about 50 nm was achieved. We analyzed the distribution of the multifunctional RNA-binding protein CELF1 on specific loops. CELF1 distribution is consistent with a model in which individual transcripts are tightly folded and hence closely packed against the loop axis.

DNA replication initiation patterns and spatial dynamics of the human ribosomal RNA gene loci

Typically, only a fraction of the ≥600 ribosomal RNA (rRNA) gene copies in human cells are transcriptionally active. Expressed rRNA genes coalesce in specialized nuclear compartments – the nucleoli – and are believed to replicate during the first half of S phase. Paradoxically, attempts to visualize replicating rDNA during early S phase have failed. Here, I show that, in human (HeLa) cells, early-replicating rDNA is detectable at the nucleolar periphery and, more rarely, even outside nucleoli. Early-replicated rDNA relocates to the nucleolar interior and reassociates with the transcription factor UBF, implying that it predominantly represents expressed rDNA units. Contrary to the established model for active gene loci, replication initiates randomly throughout the early-replicating rDNA. By contrast, mostly silent rDNA copies replicate inside the nucleoli during mid and late S phase. At this stage, replication origins are fired preferentially within the non-transcribed intergenic spacers (NTSs), and ongoing rDNA transcription is required to maintain this specific initiation pattern. I propose that the unexpected spatial dynamics of the early-replicating rDNA repeats serve to ensure streamlined efficient replication of the most heavily transcribed genomic loci while simultaneously reducing the risk of chromosome breaks and rDNA hyper-recombination.

Growth rate regulation in Escherichia coli

Growth rate regulation in bacteria has been an important issue in bacterial physiology for the past 50 years. This review, using Escherichia coli as a paradigm, summarizes the mechanisms for the regulation of rRNA synthesis in the context of systems biology, particularly, in the context of genome-wide competition for limited RNA polymerase (RNAP) in the cell under different growth conditions including nutrient starvation. The specific location of the seven rrn operons in the chromosome and the unique properties of the rrn promoters contribute to growth rate regulation. The length of the rrn transcripts, coupled with gene dosage effects, influence the distribution of RNAP on the chromosome in response to growth rate. Regulation of rRNA synthesis depends on multiple factors that affect the structure of the nucleoid and the allocation of RNAP for global gene expression. The magic spot ppGpp, which acts with DksA synergistically, is a key effector in both the growth rate regulation and the stringent response induced by nutrient starvation, mainly because the ppGpp level changes in response to environmental cues. It regulates rRNA synthesis via a cascade of events including both transcription initiation and elongation, and can be explained by an RNAP redistribution (allocation) model.

RNA dynamics in live Escherichia coli cells

We describe a method for tracking RNA molecules in Escherichia coli that is sensitive to single copies of mRNA, and, using the method, we find that individual molecules can be followed for many hours in living cells. We observe distinct characteristic dynamics of RNA molecules, all consistent with the known life history of RNA in prokaryotes: localized motion consistent with the Brownian motion of an RNA polymer tethered to its template DNA, free diffusion, and a few examples of polymer chain dynamics that appear to be a combination of chain fluctuation and chain elongation attributable to RNA transcription. We also quantify some of the dynamics, such as width of the displacement distribution, diffusion coefficient, chain elongation rate, and distribution of molecule numbers, and compare them with known biophysical parameters of the E. coli system.

Formation of circular polyribosomes in wheat germ cell-free protein synthesis system

We report a morphological study of functioning ribosomes in a efficient and robust cell-free protein synthesis system prepared from wheat embryos. Sucrose density gradient analysis of translated mixtures programmed with luciferase mRNAs having different 5' and 3' untranslated regions showed formation of large polysomes. Electron microscopic examination of translation mixtures programmed with those of capped and polyadenylated mRNA revealed that ribosomes assemble into a circular-type polysome in vitro. Furthermore, a series of experiments using mRNAs lacking either cap, poly(A) tail or both also resulted in the formation of circular polysomes, which are indistinguishable from those with the original mRNA. The wheat germ cell-free system may provide a good experimental system for understanding functional ribosomes at the molecular level.

In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes

Genes encoding rRNA are multicopy and thus could be regulated by changing the number of active genes or by changing the transcription rate per gene. We tested the hypothesis that the number of open genes is limiting rRNA synthesis by using an electron microscopy method that allows direct counting of the number of active genes per nucleolus and the number of polymerases per active gene. Two strains of Saccharomyces cerevisiae were analyzed during exponential growth: a control strain with a typical number of rRNA genes ( approximately 143 in this case) and a strain in which the rRNA gene number was reduced to approximately 42 but which grows as well as controls. In control strains, somewhat more than half of the genes were active and the mean number of polymerases/gene was approximately 50 +/- 20. In the 42-copy strain, all rRNA genes were active with a mean number of 100 +/- 29 polymerases/gene. Thus, an equivalent number of polymerases was active per nucleolus in the two strains, though the number of active genes varied by twofold, showing that overall initiation rate, and not the number of active genes, determines rRNA transcription rate during exponential growth in yeast. Results also allow an estimate of elongation rate of approximately 60 nucleotides/s for yeast Pol I and a reinitiation rate of less than 1 s on the most heavily transcribed genes.

RPD3 is required for the inactivation of yeast ribosomal DNA genes in stationary phase

rRNA transcription in Saccharomyces cerevisiae is performed by RNA polymerase I and regulated by changes in growth conditions. During log phase, approximately 50% of the ribosomal DNA (rDNA) genes in each cell are transcribed and maintained in an open, psoralen-accessible conformation. During stationary phase, the percentage of open rDNA genes is greatly reduced. In this study we found that the Rpd3 histone deacetylase was required to inactivate (close) individual rDNA genes as cells entered stationary phase. Even though approximately 50% of the rDNA genes remained open during stationary phase in rpd3Delta mutants, overall rRNA synthesis was still reduced. Using electron microscopy of Miller chromatin spreads, we found that the number of RNA polymerases transcribing each open gene in the rpd3Delta mutant was significantly reduced when cells grew past log phase. Bulk levels of histone H3 and H4 acetylation were reduced during stationary phase in an RPD3-dependent manner. However, histone H3 and H4 acetylation was not significantly altered at the rDNA locus in an rpd3Delta mutant. Rpd3 therefore regulates the number of open rDNA repeats.

EM visualization of transcriptionally active genes after injection into Xenopus oocyte nuclei

This article has described methods in use in our lab for microinjection of genes into Xenopus oocyte nuclei followed by EM visualization of those genes by the Miller chromatin spreading method. We consider our efforts to be still developing, as we attempt to maximize the visualization of specific, active, mappable genes. One of our main goals at this time is to find a DNA sequence element that will ensure efficient Pol II termination so that the common problem of read-through transcription (as seen in Fig. 6) can be overcome. We currently are testing three different elements reported to have roles in transcription termination. The method is evolving as a unique and valuable approach to study gene expression and RNA processing at the level of individual genes and individual transcripts. Given the ability to manipulate both cis- and trans-acting factors prior to EM visualization, its potential is limited only by the somewhat labor-intensive nature of the method.

Visualization of specific gene expression in individual Salmonella typhimurium cells by in situ PCR

An in situ PCR protocol by which we can monitor the presence or absence of lac mRNA in individual cells of a Salmonella typhimurium F' lac+ strain has been developed. In this protocol, fixed cells are permeabilized with lysozyme and subjected to a seminested reverse transcriptase PCR using reporter molecule-labeled primers, and subsequently, intracellular reporter molecules are detected microscopically at the individual-cell level by use of a horseradish peroxidase-conjugated antifluorescein antibody assay. In order to determine the sensitivity of the in situ PCR assay, the ability to detect lac mRNA in suboptimally isopropyl-beta-D-thiogalactopyranoside-induced cells was investigated. By use of a single-cell beta-galactosidase assay, it was confirmed that homogeneous suboptimally induced cultures of S. typhimurium F' lacY cells could be established, and the number of functional lac mRNAs in individual cells was estimated from standard population level beta-galactosidase assays. Cells estimated to contain a single lac mRNA were detected as containing lac mRNA by the in situ PCR method. Conclusively, we demonstrate the potential of in situ PCR for detection of even poorly expressed mRNA in individual bacterial cells.

Visualization of ultraviolet light-induced thymine dimers in DNA by immunoelectron microscopy

To see the damage of DNA due to ultraviolet-B more distinctly, immunoelectron microscopic studies using a monoclonal antibody against cyclobutane-type thymine dimers were performed. As a result, we could detect the existence of thymine dimers on human genomic DNA and pUC18 plasmid DNA visually. This technique can be useful to locate the photoproducts formed on DNA.

Faithful in vivo transcription termination of Xenopus laevis rDNA. Correlation of electron microscopic spread preparations with S1 transcript analysis

DNA sequencing and subsequent functional in vitro analysis of the Xenopus laevis rDNA transcription termination has led to the identification of three transcription termination sequence elements: T1, located at the 3' end of the 28S rDNA; T2, a putative processing site 235 bp downstream of T1; T3, the principal terminator positioned 215 bp upstream of the gene promoter. As demonstrated for nuclear run-off assays, T3 was found to be the main terminator for Xenopus rDNA transcription. These in vitro data are in obvious contradiction to results obtained by electron microscopic (EM) spread preparations from rapidly isolated amplified oocyte nucleoli, i.e., an rDNA chromatin probe thought to represent the in vivo situation, indicative of transcription termination at sites T1-2. However, most interestingly, T3 had--again by the EM method--been identified as the exclusive terminator for NTS spacer transcription units. In order to answer the question of whether read-through transcription of the complete rDNA spacer sequence is obligatory for 40S pre-rRNA in vivo transcription, we analyzed several hundreds of spread rRNA genes from Xenopus oocyte nucleoli in great detail, applying two different spreading procedures, e.g., dispersal of amplified oocyte nucleoli shortly in detergent-free or detergent containing low-salt media prior to the EM spreading technique. Quantitation of EM spreads resulted in the finding that read-through rDNA spacer transcription beyond T1-2 termination sites (i.e., indicative of T3 transcription termination) can be visualized for the in vivo situation at a frequency of less than 3% of rRNA genes analyzed.(ABSTRACT TRUNCATED AT 250 WORDS)

rRNA transcription rate in Escherichia coli

The rate of in vivo transcription elongation for Escherichia coli rRNA operons was determined by electron microscopy following addition of rifampin to log-phase cultures. Direct observation of RNA polymerase positions along rRNA operons 30, 40, and 70 s after inhibition of transcription initiation yielded a transcription elongation rate of 42 nucleotides per s.

EM analysis of Drosophila chorion genes: amplification, transcription termination and RNA splicing

We have used the electron microscope to examine ultrastructurally several events occurring during the biogenesis of two very abundant chorion (eggshell) mRNA molecules in the follicle cells of Drosophila melanogaster--namely, selective gene amplification, transcription initiation and termination, and RNA processing. We find that the highly transcribed s36 and s38 genes are positioned in the central region of large, multi-forked amplified DNA structures. Transcript morphology is consistent with the known presence of a small intron at the 5' end of each gene. Mature transcripts are associated with spliceosomes, demonstrating that splice site selection occurs co-transcriptionally but that splicing is completed after transcript release from the template. We have also mapped the termination sites for the genes. The two genes exhibit efficient termination very near their poly(A) sites--within a 210 bp region for s36 and a 360 bp region for s38.

Transcription mapping of the Escherichia coli chromosome by electron microscopy

The distinctive double Christmas tree morphology of rRNA operons as visualized by electron microscopy makes them easy to recognize in chromatin spreads from Escherichia coli. On the basis of the pattern of nascent transcripts on nearby transcription units and the relative distances of the operons from one another and the replication origin, we are now able to specifically identify five of the seven rRNA operons in E. coli. The use of rRNA operons as markers of both position and distance has resulted in the morphological mapping of a significant portion of the E. coli chromosome; over 600 kilobase pairs in the 84- to 90-min and 72-min regions can now be recognized. Since individual rRNA operons could be identified, direct comparisons could be made of their transcriptional activities. As judged by the densities of RNA polymerases along the operons, rrnA, rrnB, rrnC, rrnD, and rrnE were all transcribed at similar levels, with one RNA polymerase every 85 base pairs. The ability to recognize individual operons and specific regions of the chromosome allows direct comparisons of various genetic parameters.

Sensitivity of RNA synthesis to actinomycin D inhibition is dependent on the frequency of transcription: a mathematical model

The synthesis of ribosomal RNA is known to be up to 100-fold more sensitive to inhibition by actinomycin D than is messenger RNA. A model is presented here to explain the dose-response kinetics of this inhibition. The basic concept is that on very actively transcribed genes, such as ribosomal DNA, the first bound actinomycin D will sterically affect those densely packed polymerase molecules between it and the promoter, causing them to stack up into the promoter and interfere with the initiation of RNA synthesis. However, on less active genes, where the polymerases are widely spaced, the drug will inhibit individual polymerasas independently and only at the actinomycin blockade. Counteracting these inhibitory effects will be the tendency of genes bound with actinomycin to accumulate additional polymerases. A mathematical model is described which successfully explains previously reported dose-response kinetics of actinomycin inhibition in both frequently and infrequently transcribed genes. The analysis indicates that actinomycin inhibition is dependent on both polymerase packing and on gene size. The dose-response kinetics can be used to estimate both the size and transcriptional efficiency of individual genes. The model is also able to explain several other independent observations regarding the kinetics of inhibition of RNA synthesis by actinomycin.

Development of structural organization of protein-synthesizing machinery from prokaryotes to eukaryotes

Though the mechanisms of protein biosynthesis are similar in the cells of prokaryotes and eukaryotes, the eukaryotic translational machinery in the cell is arranged more intricately. One of the most striking characteristic features of the eukaryotic translational machinery is that the eukaryotic proteins involved in the translational process, such as initiation factors, elongation factors and aminoacyl-tRNA synthetases, in contrast to their prokaryotic analogs, possess a non-specific affinity for RNA. Due to the RNA-binding ability, these eukaryotic proteins can be compartmentalized on polyribosomes. In addition to the proteins of the translational apparatus, several other eukaryotic RNA-binding proteins can be also compartmentalized on polyribosomes; these proteins include glycolytic enzymes, steroid hormone receptors and intermediate filament proteins. Thus, the eukaryotic polyribosome is an element of the cytoplasmic labile structure on which various proteins can be compartmentalized and, consequently, different biochemical pathways can be integrated.

DNA synthesis in Plasmodium berghei during asexual and sexual development

DNA contents of individual stages of Plasmodium berghei were measured by direct microfluorometry after Feulgen-pararosaniline (SO2) staining. Sporozoites, intra-erythrocytic ringforms and trophozoites (until at least 15 h after invasion) are haploid and non-synthesizing DNA. DNA is synthesized just before and during schizogony, which takes 4-6 h. Genome duplication and segregation are alternating events throughout this process. Mature micro- and macrogametocytes have DNA contents between the haploid and diploid value; most, if not all of the DNA in excess of the haploid value is synthesized during the last 5-10 h of maturation. During gametogenesis microgametocytes within 8-10 min synthesize DNA steadily and at a very high rate to more than the octoploid value while the DNA content of macrogametocytes remains constant. Fertilization in vitro takes place within 1 h after gamete formation. Within 2 h and coinciding with the onset of meiosis the zygote then synthesizes DNA up to almost the tetraploid value, after which synthesis stops during ookinete development. All the above mentioned processes of DNA synthesis are reversibly inhibited by aphidicolin (C50 from 3-13 microM). From the rate of DNA synthesis during microgametogenesis we calculated a minimum of 1300 origins of replication in the haploid genome of P. berghei.

Supramolecular assemblies of mRNA direct the coordinated synthesis of type I procollagen chains

Registration of the three procollagen alpha chains and assembly of the triple-helical procollagen molecules takes place in the rough endoplasmic reticulum, but the exact location and timing of assembly is not known. As part of a study of the mechanism of molecular assembly, intact collagen-producing polyribosomes from embryonic chicken tendon fibroblasts have been examined by the techniques of rotary shadowing and electron microscopy. Intact mRNA strands corresponding in length to approximately 4500 bases and complete procollagen alpha (I) chains have been observed. The mRNA strands are comprised of two mRNA chains. The ribosomes are present in pairs separated along the duplex strand by about 100 nm. The intact polysome is asymmetric; two duplex strands join, and large ribosome aggregates appear. These aggregates are dispersed by collagenase digestion, leaving separate duplex strands with ribosome pairs intact. Ribonuclease digestion yields mixtures of monosomes and ribosome aggregates. Sequential ribonuclease and collagenase digestions yield only monosomes. We propose that each ribosome reads one mRNA chain, so that each pair is thus translating two chains in synchrony. Thus, the complex morphology of the collagen-producing polyribosomes suggests that the organization of a single molecule begins by the organization of the mRNA chains themselves.

Gene expression in the polycistronic operons of Escherichia coli heat-labile toxin and cholera toxin: a new model of translational control

A new model is proposed based on the suggestion that stable local secondary structures of mRNA interfere with ribosome movement on mRNA and consequently reduce the translation rate. This model accounts for a different level of translation for each cistron in the polycistronic mRNA of Escherichia coli heat-labile toxin (LT) and cholera toxin. We also conclude that the mRNA secondary structures have been conserved during the evolution of the toxin genes for its functional importance.

Polysome structure in sea urchin eggs and embryos: an electron microscopic analysis

Modified chromatin-spreading techniques have been used to prepare reproducible spreads of polysomes for EM visualization. We have analyzed polysomes of sea urchin (Lytechinus pictus) eggs and embryos to elucidate some of the events which occur during the burst of protein synthetic activity following fertilization. We have confirmed that the rise in protein synthesis after fertilization is concomitant with the recruitment of messenger RNA molecules into polysomes. The presence of ribosome-free tails is a structural feature of polysomes in which the mRNA is being translated for the first time. This structural marker has allowed us to derive an elongation rate of 1.5-1.8 amino acids/sec and a transit time of 5 min for the average-sized polysome in L. pictus embryos at 16 degrees C. We have also observed a difference between the structure and the average size of polysomes in the egg and embryo. Egg polysomes are longer (average size = 11.96 ribosomes, n = 671) than 1-hr embryo polysomes (average size = 7.14 ribosomes, n = 863) and 10% of the egg polysomes contain visible gaps while less than 1% of the 1-hr embryo polysomes contain internal ribosome-free regions. We speculate that such differences reflect the lower translation efficiency of the relatively dormant egg cell.

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.

Workshop no. 6. Structure, function and evolution of kinetoplast DNA

The kinetoplast DNA (kDNA) of kinetoplastidae was the first mitochondrial DNA (mtDNA) to be discovered, and with its unusual network structure, consisting of more than 104catenated DNA circles, it is without equal in nature. Analysis of networks from various genera (reviewed by Borst & Hoeijmakers (1979a) and Englund (1980)) has shown that they always consist of two components: mini-circles and maxi-circles (see Table 1). The mini-circles are the major component and deterraine the size and sliape of networks. They vary in size between 1 and 3 kilo-base pairs (kb = 1000 base pairs (bp)), they are heterogeneous in sequence, their sequence evolves rapidly and their function is not yet known. The maxi-circles, on the other hand, are homogeneous in sequence, their sequence is conserved and they probably represent the counterpart of mtDNA in other organisms.

Nature of the regions involved in the insertion of newly synthesized protein into the outer membrane of Escherichia coli

Outer membrane proteins are synthesized by cytoplasmic membrane-bound polysomes, and inserted at insertion sites which cover about 10% of the total outer membrane when cells grow with a generation time of 1 h. A membrane fraction enriched in outer membrane insertion regions was isolated and partly characterized. The rat at which newly inserted proteins are transferred from such insertion regions into the rest of the outer membrane was found to be very fast; the new protein content of insertion regions and that of the remaining outer membrane equilibrate completely within about 20 s at 25 degrees C. Given the rather rigid structure of the outer membrane and the multiple interactions between outer membrane components and the murein layer, lateral diffusion of newly inserted proteins from insertion sites to the remaining outer membrane is not likely to explain this rapid equilibration. Instead, the data support a model in which insertion regions move along the cell surface, leaving behind stationary, newly inserted outer membrane proteins.

Higher order structure in metaphase chromosomes. I. The 250 A fiber

Metaphase chromosomes released from cells in the presence of Joklik's suspension media by vortex-mixing with 0.5 mm glass beads have been analyzed by electron microscopy. In these preparations the chromosomes are composed of series of loops (200-300 A in diameter) which are, in turn, composed of closely-apposed arrays of nucleosomes. Negative-staining of these preparations has allowed the identification of several distinct patterns within the loop which appear to arise from variations in nucleosome packing. Analogous patterns are also observed in chromatin fragments generated by brief micrococcal nuclease digestion. From these data we have deduced certain features of nucleosome-nucleosome interactions in higher-ordered chromatin fibers.

Visualization of ribosomal ribonucleic acid synthesis in a ribonuclease III-Deficient strain of Escherichia coli

Transmission electron microscopy was used to examine active ribosomal ribonucleic acid (rRNA) genes in two strains of Escherichia coli: N2077, deficient in the enzyme responsible for proper cleavage of the 16S sequence from the elongating nascent rRNA transcript; and N2076, functional in ribonuclease (RNase) III activity, yet otherwise isogenic to N2077. In the strain with wild-type RNase III, double gradients corresponding to a pattern of 16S-cleavage-23S transcription were observed. However, the RNase III-deficient strain exhibited a single ribosomal gradient of approximately the same length as the combined 16S-23S gradients of the wild-type strain. When the rRNA genes were somewhat loosely packed with RNA polymerases, a few of the nascent chains in the ribosomal matrixes of the RNase III-deficient strain were cleaved, but most appeared to be unprocessed. The completed, uncleaved transcripts originating from these gradients are believed to be 30S rRNA molecules recently characterized by biochemical probes.

Chromatin ultrastructure of lower vertebrates

Meiotic and mitotic chromosomes from amphibians and snakes were studied by electron microscopy. By using water spreading, preceded by a mild NaCl pretreatment, we showed: 1. 'Beads on a string' arrangement of the chromatin fibres; 2. The presence of loops at pachytene chromomeres as well as during metaphase of both mitosis and first meiosis; 3. Transcriptional activity for non-ribosomal RNA on peripheral loops during the middle pachytene.

Size distribution of rat liver nuclear RNA containing mRNA sequences

Total rat liver poly(A)-containing polysomal mRNA was size-fractionated on polyacrylamide gels in 98% formamide. Complementary DNA (cDNA) was prepared from the 8--14-S mRNA fraction and separated into sequences representing abundant and non-abundant mRNAs. The cDNA complementary to the abundant small mRNA of the rat liver cell (approximately 20 species) was hybridized to nuclear RNA of different lengths to determine the size distribution of nuclear RNA molecules which contain these messenger sequences. It was found that: 1. All abundant 8--14-S poly(A)-containing mRNAs have larger nuclear precursor molecules; 20% of the different messenger sequences are found in nuclear RNA of several times their cytoplasmic length. 2. 70% of the mass of the examined nuclear messenger sequences is in RNA molecules of a size similar to their polysomal mRNA; 30% are in larger than 18-S RNA and 2% are between 37 S and 44 S. 3. The majority of small messenger-containing RNA molecules in the RNA prepared from isolated nuclei are of true nuclear origin, since their frequency distribution differs significantly from that of the polysomal 8--14-S mRNA.

Linkage of 5S RNA and 16S+23S RNA genes on the E. coli chromosome

Episomes carrying limited regions of the chromosome where 5S RNA genes have previously been located are described. The DNA purified from each of these episomes contains one gene per molecule for each of the three ribosomal RNA species as shown by hybridization experiments.

The structure of mesokaryote chromosome

Condensed and dispersed forms of the chromosomes of the dinoflagellate, Prorocentrum micans, deposited on grids by the microcentrifugation technique were studied by electron microscopy. In the normally condensed form, the chromosomes appear as banded rods surrounded by a peripheral cloud of partially dispersed fibers. Single fibers in these and in extensively dispersed preparations appear as smooth threads of uniform diameter (55-65 A). The chromosome fibers are contrasted by positive-group-specific stains indicating the presence of cationic moieties associated with the DNA. Occasionally Y-shaped chromosomes are seen; these may be replicating structures. These observations are in general agreement with studies of dinoflagellate chromosomes by other techniques, and provide support for the suggestion that these organisms possess a genome organization whose structure is typical of neither prokaryotes nor eukaryotes, and hence may be intermediate forms.