Morphology of transcriptional units of rDNA. Evidence for transcription in apparent spacer intercepts and cleavages in the elongating nascent RNA

Multiparameter microscopic analysis of nucleolar structure and ribosomal gene transcription

A survey of novel microscopic approaches for structural and functional analysis of subnucleolar compartments will be presented. Research on nucleolar structure and function concentrates predominantly on two distinct types of nucleoli: (1) nucleoli present during the interphase of the cell cycle in somatic tissue culture cells and (2) nucleoli present in meiotic cells, e.g. oocytes of amphibians. These nucleoli are found during meiotic prophase of oogenesis and are functional during several months of the diplotene stage of oogenesis. A further characteristic is the fact that these nucleoli are extrachromosomal, since they originate by selective ribosomal DNA (rDNA) amplification during the early pachytene stage of oogenesis. Miller-type chromatin spread preparations using transcriptionally active nucleoli, to a major part, contributed to our understanding of the structural organization of polymerase I directed pre-rRNA transcription. Although the structural organization of the template-associated pre-rRNA transcript is known in some detail from chromatin spreads, relatively little is known about structural aspects of pre-rRNA processing. In order to investigate this intriguing question in more detail, we have developed a computer-based densitometry analysis of both template-associated and template-dissociated pre-rRNA transcripts in order to follow the structural modification of pre-rRNA transcripts during processing. Another line of experiments is devoted to the in situ structure of actively transcribing genes in the nucleolus. In order to bridge the gap between light microscopy and electron microscopy we started video-enhanced light microscopical analysis of actively transcribing genes. Although the dimensions of individual spread genes are critical for detection by optical microscopy, we succeeded in obtaining the first series of images of transcribing genes in their "native' hydrated state. An additional promising type of microscopy is transmission X-ray microscopy. Recent progress in instrumentation as well as in sample preparation has allowed us to obtain the first images of density distribution within intact, fully hydrated nucleoli using amplitude-contrast and/or phase-contrast X-ray microscopy of non-contrasted, fully hydrated nucleoli at different states of transcriptional activity. Whereas the above mentioned investigations using video microscopy and X-ray microscopy are predominantly applicable to the analysis of amplified nucleoli in amphibian oocytes, which are characterized by an extremely high transcription rate of 80-90% of rDNA genes per individual nucleolus, structural analysis of the in situ arrangement of actively transcribing genes in somatic nucleoli as present in the interphase nucleus is far more difficult to perform, mainly due to the much lower number of simultaneously transcribed active genes per individual nucleolus. Visualization of actively transcribed gene clusters is approached by an integrated experimental assay using video microscopy, confocal laser scan microscopy, and antibodies against specific nucleolar proteins.

Transcription of spacer sequences flanking the rat 45S ribosomal DNA gene

The transcriptional activity of spacer sequences flanking the rat 45S ribosomal DNA (rDNA) gene were studied. Nascent RNA labeled in in vitro nuclear run-on reactions hybridized with both 5' and 3' spacer regions. The highest level of hybridization was seen with an rDNA fragment containing tandem repeats of a 130-base-pair sequence upstream of the 45S rRNA initiation site. Synthesis of RNA transcripts homologous to this internally repetitious spacer region was insensitive to high levels of alpha-amanitin, suggesting that it is mediated by RNA polymerase I. Analysis of steady-state RNA showed that these transcripts were present at extremely low levels in vivo relative to precursor rRNA transcripts. In contrast, precursor and spacer run-on RNAs were synthesized at similar levels. This suggests that spacer transcripts are highly unstable in vivo; therefore, it may be the process of transcription rather than the presence of spacer transcripts that is functionally important. Transcription in this upstream rDNA region may be involved in regulation of 45S rRNA synthesis in rodents, as has been suggested previously for frog rRNA. In addition, the presence of transcriptional activity in other regions of the spacer suggests that some polymerase I molecules may transcribe through the spacer from one 45S gene to the next on rodent rDNA.

Transcription of spacer sequences flanking the rat 45S ribosomal DNA gene

The transcriptional activity of spacer sequences flanking the rat 45S ribosomal DNA (rDNA) gene were studied. Nascent RNA labeled in in vitro nuclear run-on reactions hybridized with both 5' and 3' spacer regions. The highest level of hybridization was seen with an rDNA fragment containing tandem repeats of a 130-base-pair sequence upstream of the 45S rRNA initiation site. Synthesis of RNA transcripts homologous to this internally repetitious spacer region was insensitive to high levels of alpha-amanitin, suggesting that it is mediated by RNA polymerase I. Analysis of steady-state RNA showed that these transcripts were present at extremely low levels in vivo relative to precursor rRNA transcripts. In contrast, precursor and spacer run-on RNAs were synthesized at similar levels. This suggests that spacer transcripts are highly unstable in vivo; therefore, it may be the process of transcription rather than the presence of spacer transcripts that is functionally important. Transcription in this upstream rDNA region may be involved in regulation of 45S rRNA synthesis in rodents, as has been suggested previously for frog rRNA. In addition, the presence of transcriptional activity in other regions of the spacer suggests that some polymerase I molecules may transcribe through the spacer from one 45S gene to the next on rodent rDNA.

Spacer promoters are essential for efficient enhancement of X. laevis ribosomal transcription

The X. laevis ribosomal DNA spacer contains duplicated RNA polymerase I "spacer promoters" and an array of repeated 60/81 bp promoter-related sequences. The latter have been shown to enhance transcription from a 40S preribosomal RNA promoter in cis. Here we present evidence that at least one spacer promoter is also necessary for efficient enhancement. Deletion of the spacer promoter sequences in a construct carrying only one such promoter reduces 40S RNA transcription to approximately 10% of wild type. This effect apparently is caused by inactivation of the spacer promoter, since mutants in which 4-177 bp of the spacer promoter and adjacent sequences are deleted are functionally equivalent. Spacer promoters and 60/80 bp arrays therefore probably act together to enhance 40S pre-RNA transcription in X. laevis.

Characterization of rat ribosomal DNA. The highly repetitive sequences that flank the ribosomal RNA transcription unit are homologous and contain RNA polymerase III transcription initiation sites

The non-transcribed spacers (NTS) of the ribosomal genes of a number of organisms have been studied and were found to contain repetitive sequences. In these studies with plasmid subclones of NTS, designated p3.4, p2.6 and p1.7, which come from both 5' and 3' flanking regions of the rat ribosomal genes, respectively, it has been determined that these sequences are found elsewhere within the genome. Southern hybridization analysis has demonstrated that the 5' and 3' NTS subclones cross-hybridize, and that the cross-hybridizing regions are synonymous with the highly repetitive regions. Sequences homologous to the rat NTS were specifically localized to both 5' and 3' flanking regions as well as to a number of the introns of cloned genes including rat serum albumin, rat alpha-fetoprotein, rat casein and human serum albumin. No hybridization was detected of the 5' NTS subclone to the human Alu sequence clone, Blur 8, or to the rodent equivalent, a clone containing Chinese hamster ovary type I and II Alu sequences. However, as reported for type II Alu sequences, the subcloned rat NTS sequences contain RNA polymerase III initiation sites and also hybridize to a number of small RNAs, but not 4.5 S or 7 S RNA. Sequence analysis of two distinct repetitive regions in p1.7 has revealed a region of alternating purine-pyrimidine nucleotides, potentially of Z DNA, and stretches of repetitive sequences. The possible roles for these repetitive sequences in recombination and in maintaining a hierarchical structure for the ribosomal genes are discussed.

Transcription in cloned spacers of Xenopus laevis ribosomal DNA

Rare individuals of Xenopus laevis exhibit frequent initiation of transcription in the spacers of oocyte ribosomal DNA (rDNA). Using electron microscopy we have characterized spacer transcription in such an individual and have confirmed that the sites of transcription initiation correspond to the imperfectly duplicated promoters ("Bam islands") present in the X. laevis rDNA spacer. We have cloned a repeat unit containing a gene and a spacer from this individual and have injected the recombinant plasmid, pXlr 164, into oocytes of other X. laevis individuals. In electron microscope preparations the spacers of some of the cloned repeats were transcribed by RNA polymerase I. This demonstrates that the ability to initiate transcription at the Bam islands is a property of the spacer DNA. On pXlr 164, initiation in the spacer occurred about 5% as frequently as transcription from the gene promoter. However, transcribed spacers were as closely packed with RNA polymerase as was the gene. We conclude that polymerase I promoters may vary over a wide range in the frequency with which they "activate" but that once activated all can load polymerases to maximal density. The presence or absence of spacer transcription had no observable effect on either the frequency of activation or the density of polymerase loading of the gene immediately downstream. A subclone, pXlr 264, containing only spacer DNA also showed regular initiation and termination, providing further evidence that there is an effective "fail-safe" termination signal 225 base pairs upstream from the rRNA gene initiation site.

Altered structure of ribosomal RNA transcription units in hamster cells after DRB treatment

The adenosine analog 5,6 dichloro-1-beta-ribofuranosyl benzimidazole (DRB) inhibits specifically mRNA production in eukaryotic cells, with concomitant alterations in pre-rRNA processing and nucleolar ultrastructure. We have focused our analysis on the effects of drug treatment on rRNA transcription through observations of spread ribosomal RNA (rRNA) transcription units from hamster cells. A significant increase in the size of ribosomal matrix units is paralleled by the appearance of abnormally large RNP structures containing elongating pre-rRNA. These structures correspond to nucleolar perichromatin granules which are known to appear in various conditions of cell growth when rRNA processing is altered. It is proposed that DRB-induced impairments in rRNA maturation are largely determined by alterations in the rRNA transcription process.

Identification and sequence of the initiation site for rat 45S ribosomal RNA synthesis

The transcription initiation site for rat 45S precursor ribosomal RNA synthesis was determined by nuclease protection mapping with two single-strand endonucleases. S1 and mung bean, and one single-strand exonuclease, ExoVII. These experiments were performed with end-labeled ribosomal DNA from double-stranded pBR322 recombinants and from single-stranded M13 recombinants. Results from experiments using both kinds of DNA and all three enzymes showed that the 5' end of 45S RNA mapped to a unique site 125 bases upstream from the Hind III site in the ribosomal DNA gene. The DNA surrounding this site (designated +1) was sequenced from -281 to +641. The entire sequence of this region shows extensive homology to the comparable region of mouse. This includes three stretches of T residues in the non-coding strand between +300 and +630. Two sets of direct repeats adjacent to these T-rich regions are observed. Comparison of the mouse and human ribosomal DNA transcription initiation sites with the rat sequence reported in this paper demonstrates a conserved sequence at +2 to +16, CTGACACGCTGTCCT. This suggests that this region may be important for the initiation of transcription on mammalian ribosomal DNAs.

A transcriptional function for the repetitive ribosomal spacer in Xenopus laevis

The function of the Xenopus laevis ribosomal spacer has been studied in vivo and by microinjection of in vitro mutants into Xenopus oocytes. It is shown that the spacer directs specific RNA transcripts which most probably terminate upstream of the ribosomal genes and that it is able to modulate transcription of these genes. The data lead to a model in which the ribosomal spacer is a loading site for RNA polymerase I and spacer transcription is the driving force by which polymerase is delivered to the ribosomal gene promoter.

Accurate transcription of cloned Xenopus rRNA genes by RNA polymerase I: demonstration by S1 nuclease mapping

We have demonstrated faithful transcriptional initiation of cloned Xenopus rRNA genes upon injection into Xenopus oocytes. This observation has been made possible by the use of an S1 nuclease assay that is both sensitive and quantitative. In order to detect rRNA synthesis from the injected template above the large background of rRNA endogenously present in oocytes, the divergence of ribosomal DNA sequences between two Xenopus species was utilized. Cloned X. laevis ribosomal DNA was injected into the nuclei of X. borealis oocytes. Total oocyte RNA was then isolated and hybridized to a radioactive DNA probe that over laps the 5' end of X. laevis rRNA; endogenous rRNA of the X. borealis oocytes does not hybridize to the probe. RNA/DNA hybrids were treated with S1 nuclease and protected fragments were sized by polyacrylamide gel electrophoresis. RNA made from the injected rDNA protects the same region of probe as does authentic X. laevis precursor rRNA. Thus, transcription appears to initiate on the cloned, microinjected X. laevis rDNA at the same site as is used in vivo. This synthesis is not impaired by coinjection of an amount of alpha-amanitin sufficient to inhibit RNA polymerase II and III; therefore the reaction is mediated by RNA polymerase I. The amount of transcription may be reproducibly quantitated and we have varied a number of parameters in order to maximize transcriptional expression of the injected rDNA. Eight independently isolated X. laevis rDNA clones as well as several subcloned initiation regions of these genes are all accurately transcribed at approximately equal efficiency. This assay should facilitate analysis of several aspects of rRNA transcription, including deleniation of the Xenopus RNA polymerase I promoter location.

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.

Identification of a novel class of tandemly repeated genes transcribed on lampbrush chromosomes of Pleurodeles waltlii

Electron microscope preparations of lampbrush chromosomes from oocytes of Pleurodeles waltlii have revealed a new class of tandemly repeated genes. These genes are highly active, as judged by the close spacing of nascent transcripts. They occur in clusters of greater than 100 copies and are transcribed in units containing roughly 940 base pairs of DNA that are separated by nontranscribed spacers of an estimated DNA content of 2,410 base pairs. The size and the pattern of arrangement of these transcription units can not be correlated with any of the repetitious genes so far described.

DNA electron microscopy

In recent years DNA electron microscopy has become a tool of increasing interest in the fields of molecular genetics and molecular and cell biology. Together with the development of in vitro recombination and DNA cloning, new electron microscope techniques have been developed with the aim of studying the structural and functional organization of genetic material. The most important methods are based on nucleic acid hybridizations: DNA-DNA hybridization (heteroduplex, D-loop), RNA-DNA hybridization (R-loop), or combinations of both (R-hybrid). They allow both qualitative and quantitative analysis of gene organization, position and extension of homology regions, and characterization of transcription. The reproducibility and resolution of these methods make it possible to map a specific DNA region within 50 to 100 nucleotides. Therefore they have become a prerequisite for determining regions of interest for subsequent nucleotide sequencing. Special methods have been developed also for the analysis of protein-DNA interaction: e.g., direct visualization of specific protein-DNA complexes (enzymes, regulatory proteins), and analysis of structures with higher complexity (chromatin, transcription complexes).

Multiple ribosomal gene sites revealed by in situ hybridization of Xenopus rDNA to Triturus lampbrush chromosomes

A variety of 3H-labelled ribosomal gene probes were hybridized in situ to the nascent transcripts of lampbrush chromosomes from the crested newt, Triturus cristatus carnifex. The probes were from Xenopus laevis and included rDNA isolated by CsCl gradient centrifugation, recombinant plasmids and purified restriction fragments of rDNA. All the probes gave essentially the same result. About 10-15 loop pairs were distinctly labelled in each preparation, almost all of them located on the heteromorphic arms (HTAs) of chromosome 1. Ribosomal gene probes were also hybridized in situ to the DNA of denatured mitotic chromosomes from some of the individuals used to provide lampbrush preparations. Minor, scattered sites of hybridization were found in the HTAs, but the main clusters of ribosomal genes were found on chromosomes 6 and/or 9, in agreement with previous determinations of nucleolus organizer position in this species. However, the nucleolus organizers were not sites of labelled loops in lampbrush transcript hybridizations.--We have incubated isolated lampbrush-stage nuclei in media containing alpha-amanitin and labelled RNA precursors. Although extrachromosomal nucleolar genes incorporated label, supposedly due to transcription by RNA polymerase I, no lampbrush loops were labelled.--It appears that in T. c. carnifex there are ribosomal gene sequences at the main nucleolus organizers and at a number of sites scattered along the HTAs. The ribosomal genes at the nucleolus organizers are not extended in the form of actively transcribing loops unlike the ribosomal sequences on the HTAs, which are heavily labelled in transcript hybridization. The ribosomal sequences on the HTAs appear not to be transcribed by the same RNA polymerase that transcribes the ribosomal genes of extrachromosomal nucleoli.

Transcriptionally active and inactive regions of nucleolar chromatin in amplified nucleoli of fully grown oocytes of hibernating frogs, Rana pipiens (Amphibia, Anura). A quantitative electron microscopic study

Chromatin structures contained in nuclei of full-grown oocytes of hibernating northern leopard frogs, Rana pipiens, kept at 4 degrees C were examined by light and electron microscopy, with special emphasis on the morphology of spread nucleoli. Light microscopic inspection of the in situ arrangement revealed that at this stage of oogenesis the numerous amplified nucleoli, together with the chromosomes, were included in a centrally located aggregate. Characteristically, the nucleoli appeared spheroidal and showed large size differences; many of them revealed a caveolated interior and close association with large dense bodies of granular (GDB) or fibrillar (FDB) substructure. A spreading procedure involving limited dispersal of nucleolar chromatin allowed the analysis of a large number of individual nucleoli from a specific nucleus. Electron microscopy showed that different types of nucleoli which could be distinguished in terms of transcriptional activity occurred in the same nucleus: (i) Nucleoli in which nearly all pre-rRNA gene regions appeared as fully covered by lateral fibrils, indicative of active transcription ('active nucleoli'); (ii) nucleoli that contained exclusively or predominantly chromatin strands free of lateral fibrils and were characterized by a uniformly beaded appearance, interpreted as transcriptionally inactive, nucleosome-packed chromatin ('inactive nucleoli'); and (iii) nucleoli in which a number of typical arrays of lateral fibril gradients occurred besides other regions that were free of such fibrils and apparently non-transcribed ('partly inactive nucleoli'). Quantitative evaluations of the proportions of active and inactive nucleolar chromatin indicated that a minimum of 70% of nucleolar DNA is not transcribed at this stage of oogenesis. Details of the pattern and ultrastructural organization of active and inactive chromatin regions are presented. Lampbrush chromosome structures were observed in the same nuclei and also showed transcriptional structures, though often with reduced packing density of lateral fibrils. The observations show that a number of genes of both kinds, those coding for pre-rRNAs and those coding for proteins, are transcribed in full-grown oocytes of hibernating frogs at 4 degrees C. However, the data also indicate that the number of transcribed genes and the frequency of transcriptional events are greatly reduced at this stage of oogenesis, especially in the nucleolar chromatin.

Changes of nucleosome frequency in nucleolar and non-nucleolar chromatin as a function of transcription: an electron microscopic study

The morphology of nucleolar and non-nucleolar (lampbrush chromosome loops) chromatin was studied in the electron microscope during states of reduced transcriptional activity in amphibian oocytes (Xenopus laevis, Triturus alpestris, T. cristatus). Reduced transcriptional activity was observed in maturing stages of oocyte development and after treatment with an inhibitor, actinomycin D. Strands of nucleolar chromatin appear smooth and thin, and contain only few, if any, nucleosomal particles in the transcribed units. This is true whether they are densely or only sparsely covered with lateral ribonucleoprotein fibrils. This smooth and non-nucleosomal character is also predominant in the interspersed, apparently nontranscribed rDNA spacer regions. During inactivation, however, nucleolar chromatin frequently and progressively assumes a beaded appearance in extended fibril-free--that is, apparently nontranscribed--regions. In either full-grown oocytes or late after drug treatment, most of the nucleolar chromatin is no longer smooth and thin, but rather shows a beaded configuration indistinguishable from inactive non-nucleolar chromatin. In many chromatin strands, transitions of fibril-associated regions of smooth character into beaded regions without lateral fibrils are seen. Similarly, in the non-nucleolar chromatin of the retracting lampbrush chromosome loops, reduced transcriptional activity is correlated with a change from smooth to beaded morphology. Here, however, beaded regions are also commonly found interspersed between the more or less distant bases of the lateral fibrils, the putative transcriptional complexes. In both sorts of chromatin, detergents (in particular Sarkosyl) that remove most of the chromatin proteins including histones from the DNA axis but leave the RNA polymerases of the transcriptional complexes attached were used to discriminate between polymerases and nucleosomal particles. The results suggest that nucleosomes are absent in heavily transcribed chromatin regions but are reformed after inactivation. In contrast to the findings with inactivated nucleolar genes, in lampbrush chromosome loops the beaded nucleosomal configuration appears to be assumed also in regions within transcriptional units that, perhaps temporarily, are not involved in transcription.

Frequencies of circular units of nucleolar DNA in oocytes of two insects, Acheta domesticus and dytiscus marginalis, and changes of nucleolar morphology during oogenesis

The organization of the extrachromosomal nucleolar material in oocytes of two insect species with different ovary types, the house cricket Acheta domesticus (panoistic ovary) and the water beetle Dytiscus marginalis (meroistic ovary), was studied with light and electron microscopic techniques. Stages early in oogenesis were compared with fully vitellogenic stages (mid-to-late diplotene). The arangement of the nucleolar material undergoes a marked change from a densely aggregated to a dispersed state. The latter was characterized by high transcriptional activity. In spread and positively stained preparations of isolated nucleolar material, a high frequency of small circular units of transcribed rDNA was observed and rings with small numbers (1--5) of pre-rRNA genes were predominant. The observations suggest that the 'extra DNA body' observed in early oogenic stages of both species represents a dense aggregate ofnumerous short circular units of nucleolar chromatin, with morphological subcomponents identifiable in ultrathin sections. These apparently remain in close association with the chromosomal nucleolar organizer(s). The observations further indicate that the individual small nucleolar subunit circles dissociate and are dispersed as actively transcribed rDNA units later in diplotene. The results are discussed in relation to principles of the ultrastructural organization of nucleoli in other cell types as well as in relation to possible mechanisms of gene amplification.

Lengths and patterns of transcriptional units in the amplified nucleoli of oocytes of Xenopus laevis

Transcriptionally active chromatin from peripheral amplified nucleoli of lampbrush-chromosome stage oocytes of Xenopus laevis was dispersed and spread in various solutions of low salt concentrations (including some with additions of detergents) and examined by electron microscopy. Nucleolar material from oocytes of animals with normal (2-nu) and mutant (1-nu) genetical constitution of nucleolus organizers was compared. Histograms showing the distributions of the length of matrix units, apparent spacer intercepts, and the total repeating units of the rDNA containing chromatin axes revealed a significant degree of heterogeity, with indications of subclasses and predominant repeat unit size classes of 3.3 amd 3.8 micron length. The correspondence of matrix unit length to the molecular weight of the first stable product of rDNA transcription was studied using gel electrophoresis of labelled pre-rRNA under non-denaturing and denaturing conditions. Evaluations of individual strands of nucleolar chromatin further demonstrated the existence of both (i) strands with obviously homogeneous repeating units of and (ii) strands with intra-axial heterogeneity of rDNA subunits. "Prelude complexes", i.e. groups of transcriptional complexes in apparent spacer intercepts, were not infrequently noted. The data are compared with the measurements of lengths of repeating units in fragments of rDNA obtained by digestion with EcoRI endonuclease as described by Morrow et al.(1974) and Wellauer et al. (1974,1976a, b). The results are discussed in relation to problems of variations in the modes of arrangement of the pre-rRNA genes, the state of packing of rDNA during transcription, and possible mechanisms of the amplification process.