Gene linkage by RNA-DNA hybridization. I. Unique DNA sequences homologous to 4 s RNA, 5 s RNA and ribosomal RNA

Nuclear routing networks span between nuclear pore complexes and genomic DNA to guide nucleoplasmic trafficking of biomolecules

In health and disease, biomolecules, which are involved in gene expression, recombination, or reprogramming have to traffic through the nucleoplasm, between nuclear pore complexes (NPCs) and genomic DNA (gDNA). This trafficking is guided by the recently revealed nuclear routing networks (NRNs).In this study, we aimed to investigate, if the NRNs have established associations with the genomic DNA in situ and if the NRNs have capabilities to bind the DNA de novo. Moreover, we aimed to study further, if nucleoplasmic trafficking of the histones, rRNA, and transgenes' vectors, between the NPCs and gDNA, is guided by the NRNs.We used Xenopus laevis oocytes as the model system. We engineered the transgenes' DNA vectors equipped with the SV40 LTA nuclear localization signals (NLS) and/or HIV Rev nuclear export signals (NES). We purified histones, 5S rRNA, and gDNA. We rendered all these molecules superparamagnetic and fluorescent for detection with nuclear magnetic resonance (NMR), total reflection x-ray fluorescence (TXRF), energy dispersive x-ray spectroscopy (EDXS), and electron energy loss spectroscopy (EELS).The NRNs span between the NPCs and genomic DNA. They form firm bonds with the gDNA in situ. After complete digestion of the nucleic acids with the RNases and DNases, the newly added DNA - modified with the dNTP analogs, bonds firmly to the NRNs. Moreover, the NRNs guide the trafficking of the DNA transgenes' vectors - modified with the SV40 LTA NLS, following their import into the nuclei through the NPCs. The pathway is identical to that of histones. The NRNs also guide the trafficking of the DNA transgenes' vectors, modified with the HIV Rev NES, to the NPCs, followed by their export out of the nuclei. Ribosomal RNAs follow the same pathway.To summarize, the NRNs are the structures connecting the NPCs and the gDNA. They guide the trafficking of the biomolecules between the NPCs and the gDNA.

Journey of a Molecular Biologist

My journey into a research career began in fermentation biochemistry in an applied science department during the difficult post-World War II time in Japan. Subsequently, my desire to do research in basic science developed. I was fortunate to be a postdoctoral fellow in the United States during the early days of molecular biology. From 1957 to 1960, I worked with three pioneers of molecular biology, Sol Spiegelman, James Watson, and Seymour Benzer. These experiences helped me develop into a basic research scientist. My initial research projects at Osaka University, and subsequently at the University of Wisconsin, Madison, were on the mode of action of colicins as well as on mRNA and ribosomes. Following success in the reconstitution of ribosomal subunits, my efforts focused more on ribosomes, initially on the aspects of structure, function, and in vitro assembly, such as the construction of the 30S subunit assembly map. After this, my laboratory studied the regulation of the synthesis of ribosomes and ribosomal components in Escherichia coli. Our achievements included the discovery of translational feedback regulation of ribosomal protein synthesis and the identification of several repressor ribosomal proteins used in this regulation. In 1984, I moved to the University of California, Irvine, and initiated research on rRNA transcription by RNA polymerase I in the yeast Saccharomyces cerevisiae. The use of yeast genetics combined with biochemistry allowed us to identify genes uniquely involved in rRNA synthesis and to elucidate the mechanism of initiation of transcription. This essay is a reflection on my life as a research scientist.

Transcriptional origin of Euglena chloroplast tRNAs

tRNA.DNA hybridization studies indicate that Euglena chloroplast tRNAs are transcriptional products of the chloroplast genome, which contains approximately 26 tRNA cistrons. Hybridization with purified chloroplast tRNA(Phe) and tRNA(Asp) shows that the chloroplast genome contains one cistron for each of these two species. No hybridization of chloroplast tRNA with nuclear DNA was observed. tRNAs from Euglena cytoplasm, Escherichia coli, and Agmenellum quadraduplicatum do not compete with chloroplast tRNA for hybridization with chloroplast DNA. Evidence is presented that photoinduction of chloroplast tRNAs is at the level of transcription rather than maturation of tRNA precursor molecules.

Xenopus transcription factor IIIA and the 5S nucleosome: development of a useful in vitro system

5S RNA genes in Xenopus are regulated during development via a complex interplay between assembly of repressive chromatin structures and productive transcription complexes. Interestingly, 5S genes have been found to harbor powerful nucleosome positioning elements and therefore have become an important model system for reconstitution of eukaryotic genes into nucleosomes in vitro. Moreover, the structure of the primary factor initiating transcription of 5S DNA, transcription factor IIIA, has been extensively characterized. This has allowed for numerous studies of the effect of nucleosome assembly and histone modifications on the DNA binding activity of a transcription factor in vitro. For example, linker histones bind 5S nucleosomes and repress TFIIIA binding in vitro in a similar manner to that observed in vivo. In addition, TFIIIA binding to nucleosomes assembled with 5S DNA is stimulated by acetylation or removal of the core histone tail domains. Here we review the development of the Xenopus 5S in vitro system and discuss recent results highlighting new aspects of transcription factor - nucleosome interactions,

The dawn of gene isolation

Ever since it became clear through the work of Watson and Crick that the gene is a stretch of double stranded helical DNA and is understandable in chemical terms, biochemists have striven to get their hands on isolated genes. The isolation of the ribosomal genes of Xenopus laevis in 1966 provided a first instance where a purified DNA of known function could be investigated, long before the advent of gene cloning technologies. The second instance was the purification of the Lac operon from Escherichia coli. Later, but still before the gene cloning days the 5S RNA genes of X. laevis and the histone genes of the sea urchin Psammechinus miliaris were isolated by physico-chemical methods, but their isolation marked the end of an era. By 1975, gene cloning technology was well established and the isolation of genes quickly became an everyday occurrence.

Small nucleolar RNAs and nucleolar proteins in Xenopus anucleolate embryos

We investigated the presence and localization, in the cells of anucleolate mutant embryos of Xenopus laevis, of three representative small nucleolar RNAs (snoRNAs), U3, U15 and U17, and of two nucleolar proteins, nucleolin and fibrillarin. The levels of the three snoRNAs in the anucleolate mutant are the same as in normal embryos, in contrast to 5S RNA and ribosomal proteins. In situ hybridization showed that, in the absence of fully organized nucleoli, the three RNAs are diffusely distributed in the nucleus and partly associated with a number of small structures. Nucleolin and fibrillarin are also present in the anucleolate embryos as in normal embryos, although there is less nucleolin mRNA in the former. The two nucleolar proteins were localized by immunofluorescence microscopy. Fibrillarin, similar to its associated U3 and U15 snoRNAs, is diffusely distributed in the anucleolate nucleus and is partly associated with small structures, probably prenucleolar bodies and pseudonucleoli. Nucleolin also appears diffusely distributed in the nucleus with some spots of higher concentration, but with a different pattern with respect to fibrillarin.

"Micronucleoli" in the Xenopus germinal vesicle

The germinal vesicle of the Xenopus oocyte contains 1500 or more extrachromosomal nucleoli that are assembled on amplified copies of the rRNA genes. Many of these nucleoli have diameters of 10-15 micron, but some are much smaller, ranging down to 1 micron or less. Morphologically the smaller nucleoli or "micronucleoli" resemble the similarly sized B snurposomes, but they can be recognized with appropriate antibody probes (e.g., anti-nucleolin and anti-fibrillarin). We describe here a sensitive fluorescent staining technique that uses avidin and propidium iodide to visualize the rDNA in the amplified nucleoli. Many large nucleoli stain about as brightly as haploid yeast nuclei on the same slides. They presumably contain about 12 Mb of DNA, equivalent to 900 rDNA repeats. The smallest micronucleoli display only a tiny dot of stain, which must correspond to relatively few rDNA repeats.

Structure and expression of ribosomal protein genes in Xenopus laevis

In Xenopus laevis, as well as in other vertebrates, ribosomal proteins (r-proteins) are coded by a class of genes that share some organizational and structural features. One of these, also common to genes coding for other proteins involved in the translation apparatus synthesis and function, is the presence within their introns of sequences coding for small nucleolar RNAs. Another feature is the presence of common structures, mainly in the regions surrounding the 5' ends, involved in their coregulated expression. This is attained at various regulatory levels: transcriptional, posttranscriptional, and translational. Particular attention is given here to regulation at the translational level, which has been studied during Xenopus oogenesis and embryogenesis and also during nutritional changes of Xenopus cultured cells. This regulation, which responds to the cellular need for new ribosomes, operates by changing the fraction of rp-mRNA (ribosomal protein mRNA) engaged on polysomes. A typical 5' untranslated region characterizing all vertebrate rp-mRNAs analyzed to date is responsible for this translational behaviour: it is always short and starts with an 8-12 nucleotide polypyrimidine tract. This region binds in vitro some proteins that can represent putative trans-acting factors for this translational regulation.

Amphibian oocytes and sphere organelles: are the U snRNA genes amplified?

The sphere organelles (spheres) of Xenopus and other amphibian oocytes are known to contain small nuclear ribonucleoprotein particles (snRNPs) and have been suggested to play a role in snRNP complex assembly. Coupled with the similarities that exist between spheres and nucleoli and the quantitative and kinetic aspects of snRNA synthesis in the Xenopus oocyte, we have investigated whether or not the U snRNA encoding genes are amplified in Xenopus oogenesis, the spheres being possible sites for the location of such extrachromosomal gene copies. By applying a number of quantitative nucleic acid hybridization procedures to both total and fractionated oocyte and somatic DNA, employing both homologous and heterologous U snRNA gene probes and suitable amplification and non-amplification control probes, we show that the U snRNA genes do not undergo any major amplification in Xenopus oogenesis. Therefore, the analogy between the sphere organelles and nucleoli appears to be limited. The role of the spheres and their relationship to other snRNP containing structures, specifically B snurposomes, and the sphere organizer loci remains obscure.

Xenopus laevis in developmental and molecular biology

Xenopus laevis is a prime system for the study of embryogenesis in vertebrates. Both prelocalized information in the egg and inductive interactions between cells contribute to the ordered increase in complexity during development. Embryonic induction, discovered in amphibians, is being studied intensely in Xenopus; recent work suggests a role for growth factors in this process. Contributions of the Xenopus system to the analysis of ribosomal and 5S RNA genes, and the diverse and highly productive applications of the oocyte injection technology, are also summarized.

Sequence and transcription of tRNAVal gene from Xenopus laevis

A DNA fraction enriched in tRNA genes has been prepared by CsCl density gradient centrifugation of Xenopus laevis DNA in the presence of actinomycin D. This DNA fraction was cut with the restriction endonuclease EcoRI and the fragments 800-900 base pairs in size were cloned into the plasmid pBR325. Recombinant DNAs were screened by hybridization to labeled tRNA and for the ability to support transcription in vitro. The entire sequence of one fragment was determined by sequencing the ends of an overlapping set of deletion fragments. A sequence homologous to tRNAVal from mammalian sources was found in this fragment and it was shown that this sequence corresponds to the region of the fragment that is transcribed. The cloned fragment was also transcribed in vivo after injection into X. laevis oocytes. The RNA that was synthesized in the oocytes was digested with ribonuclease T1 and the oligonucleotides were separated to produce a two-dimensional fingerprint. The results of the analysis of the oligonucleotides are consistent with the sequence determined for the tRNAVal gene. The X. laevis genome has 200-250 copies of the 892 base pair EcoRI fragment and additional copies of a 4100 base pair EcoRI fragment that each contain a tRNAVal gene. Digestion of X. laevis DNA with several other restriction endonucleases reveals that the cloned fragment that contains the tRNAVal gene is part of a longer sequence element that is tandemly repeated in the genome.

Structural analysis of ribosomal DNA homologues in nucleolus-less mutant of Xenopus laevis

Sequences homologous to the ribosomal DNA (rDNA) in a Xenopus anucleolate (nucleolus-less) mutant were analyzed by Southern blot analysis. The mutant was found to possess a variety of sequences homologous to non-transcribed spacer (NTS) and/or coding region of rDNA. 65 rDNA-homologous clones were isolated from a genomic DNA library of the mutant. All the clones showed only partial homology to the normal rDNA unit and their restriction maps differed from that of the normal rDNA unit. Based on the hybridization patterns, the rDNA-homologous clones were divided into four groups (I-IV). Structure of group IV, which most strongly hybridized to normal rDNA probe, was analyzed by nucleotide sequencing. The group IV sequence was found to contain a part of the rDNA, including Bam island, enhancer element, promoter region, external transcribed spacer, and a portion of 18S rRNA gene. The blotting analysis suggested that the group IV sequence is specific for a particular strain of Xenopus.

Molecular organization of ribosomal RNA genes clustered at variable chromosomal sites in Triturus vulgaris meridionalis (Amphibia, Urodela)

The ribosomal RNA genes of Triturus vulgaris meridionalis (Amphibia, Urodela) show the peculiar feature of being clustered not only at the nucleolar organizer, present in the species at a definite chromosome location, but also at "additional ribosomal sites" which are highly variable in number and chromosomal distribution among individuals. The additional ribosomal sites are most often found at specific chromosome regions, such as telomeres, C-bands and centromeres, in virtually all the chromosomes. With increasing numbers of additional clusters, the genomic dosages of ribosomal RNA genes are found to increase over a tenfold range, though not linearly. At a molecular level, the ribosomal DNA repeats differ in size because of discrete variations in the length of the non-transcribed spacers. However, the resulting length heterogeneity of the gene family is rather limited within a single genome as well as within the species. Many of the ribosomal loci appear to be internally homogeneous with respect to the repeat length. Moreover, separate clusters from distant genomic regions can share the same size class of ribosomal repeats even in the same specimen. The nucleolar organizer is mostly endowed with "shorter" ribosomal repeating units, ranging in size from 13.7 X 10(3) to 15.2 X 10(3) base-pairs. The additional ribosomal sites are characterized by the occurrence of "longer" repeats, ranging in size from 16.2 X 10(3) to 19.7 X 10(3) base-pairs. The "shorter" class of ribosomal repeats is always detected in the amplified ribosomal DNA, suggesting that the nucleolar organizer locus is involved in the amplification process in most oocytes. "Longer" ribosomal repeats are also detectable in the amplified ribosomal DNA of a few females.

Quantitative variation in components of the maize mitochondrial genome between tissues and between plants with different male-sterile cytoplasms

The amounts of a 1.9 kb mitochondrial plasmid relative to sequences in another mitochondrial DNA replicon and also to nuclear ribosomal DNA sequences have been compared in maize leaves and anthers. Similar comparisons have been made between plants with the same nuclear genotype but containing normal, S, or T cytoplasms. The ratio of 1.9 kb plasmid to nuclear rDNA is lower in plants with normal cytoplasm than in plants with S or T cytoplasm. It also differs between leaves and anthers. Furthermore, the relative concentration of the mitochondrial DNA sequences belonging to different replicons differs between leaves and anthers. It is concluded that components of different mitochondrial replicons are not maintained in fixed ratios during development and that the concentration of the 1.9 kb plasmid is regulated, in part, by cytoplasmically-inherited determinants. The 1.9 kb plasmid is absent from lines with the Vg cytoplasm, but related sequences are found in the maize nuclear genome.

Analysis of genes for 5S rRNA from the cricket, Acheta domesticus: two classes of repeating units

To examine the modulation of 5S rRNA gene activity during development in the cricket, Acheta domesticus, 5S X DNA was isolated from a lambda Charon 4 genomic library and characterized. Southern blot analysis of cloned A. domesticus genomic DNA revealed that restriction fragments of 3.0 and 2.1 kb represent two size classes of 5S X DNA repeating units; over 90% of the repeats measure 3.0 kb. Restriction analysis of two 5S X DNA clones suggests that the 2.1-kb repeats are not randomly interspersed within clusters of the larger 3.0-kb repeating units. Heteroduplex and restriction mapping of several clones indicate that the spacers of both repeating units account for their unusual length. The major difference between the two classes of repeats may lie in 0.9-kb spacer sequences to the 3.0-kb repeats.

Distribution and utilization of 5 S-RNA-binding proteins during the development of Xenopus oocytes

At early stages of oogenesis in Xenopus laevis most of the ribosomal 5S RNA is complexed with three proteins to form two types of cytoplasmic RNP storage particle. A particle sedimenting at 42S contains 5S RNA and tRNA together with two proteins of Mr 48000 (P48) and Mr 43000 (P43) and a second particle sedimenting at 7S contains 5S RNA plus a protein of Mr 40000 (P40, also known as the transcription factor, TFIIIA). In this report we use antibodies monospecific for each protein to follow the movement of 5S RNA from nucleus to cytoplasm to nucleolus to cytoplasm and to determine the fate of each of the proteins that associate with 5S RNA during these transitions. Both P48 and P43 have roles additional to the formation of the 42S RNP storage particle; P48 is detected in the nucleus during early oogenesis and is cleaved to yield an Mr-33000 fragment that remains associated with 5S RNA that is excess to ribosome requirement during late oogenesis; P43 appears to be cleaved to yield fragments of Mr 28000 and 17000, the latter being present in ribosomal fractions. Apparently, there is no function for P40 in addition to those already described in transcription of 5S RNA genes and in storage of 5S RNA as a 7S RNP particle.

Genetic recombination of Xenopus laevis 5 S DNA in bacteria

The behavior in genetic recombination of Xenopus laevis 5 S DNA has been examined, with particular emphasis on the role of 15-base-pair tandem repeats in the A + T-rich spacer. Fragments of 5 S DNA were introduced into Escherichia coli cells as inserts in the recombination vectors, lambda rva and lambda rvb. Intermolecular recombinants were selected in which, because of properties of the phage vectors, the crossover event must have occurred within the 5 S DNA inserts. Inserts from individual recombinants have been characterized in detail. The effects of varying the number (n) of 15-base-pair repeats and the recombination capabilities of the phage and host have been investigated. In these crosses, unequal crossovers can occur, yielding inserts different in size from the parental inserts. When the number of 15-mers is large (n = 12 or 20), most of the unequal crossovers have occurred within the 15-mers, resulting in an altered n value, although other homologies within the 5 S DNA sequence can also support unequal events. Increasing n in the parental inserts modestly increases the overall frequency of recombination and the percentage of altered inserts. We conclude that, in a bacterial setting, the 15-base-pair repeats stimulate recombination only slightly by allowing alternative registers for heteroduplex formation. The degree of stimulation observed is less than predicted by one simple model.

Anucleolate frog embryos contain ribosomal DNA sequences and a nucleolar antigen

Previous studies of Xenopus laevis embryos homozygous for the nucleolar deletion mutation have concluded that these embryos contain few, if any, copies of the genes for the 18 S and 28 S ribosomal RNAs. Using hybridization to restriction endonuclease digests of DNA it is found, in fact, that a small amount of ribosomal DNA is still present in such embryos. The ribosomal DNA in these embryos appears to include a few normal repeats together with a variety of unusual fragments containing either spacer or gene sequences. An antibody found in the serum of a scleroderma patient reacts with an antigen localized in the nucleoli of wild-type embryos. In anucleolate embryos this antigen is found in the so-called pseudonucleoli and in many small bodies in the nuclei.

Nuclear exclusion of transcription factor IIIA and the 42s particle transfer RNA-binding protein in Xenopus oocytes: a possible mechanism for gene control?

The intracellular location of 7S and 42S RNP particles in Xenopus oocytes has been determined by immunohistochemistry. Using antibodies directed against the 48-mol-wt protein component of the 42S particle and against transcription factor IIIA, the protein moiety of the 7S particle, we show that these ribonucleoprotein particles are detectable only in the oocyte cytoplasm, being excluded from the nucleus. The mechanism of this nuclear exclusion, and its possible significance in the regulation of 5S RNA gene expression, are discussed.

Regular arrangement of nucleosomes on 5S rRNA genes in Xenopus laevis

The chromatin structure of the oocyte-type 5S RNA genes in Xenopus laevis was investigated. Blot hybridization analysis of DNA from micrococcal nuclease digests of erythrocyte nuclei showed that 5S DNA has the same average nucleosome repeat length, 192 +/- 4 base pairs, as two Xenopus satellite DNAs and bulk erythrocyte chromatin. The positions of nuclease-sensitive regions in the 5S DNA repeats of purified DNA and chromatin from erythrocytes were mapped by using an indirect end-labeling technique. Although most of the sites cleaved in purified DNA were also cleaved in chromatin, the patterns of intensities were strikingly different in the two cases. In 5S chromatin, three nuclease-sensitive regions were spaced approximately a nucleosome length apart, suggesting a single, regular arrangement of nucleosomes on most of the 5S DNA repeats. The observed nucleosome locations are discussed with respect to nucleotide sequences known to be important for expression of 5S RNA. Because the preferred locations appear to be reestablished in each repeating unit, despite spacer length heterogeneity, we suggest that the regular chromatin structure reflects the presence of a sequence-specific DNA-binding component on inactive 5S RNA genes.

Stain intensity of human nucleolus organizer region reflects incorporation of uridine into mature ribosomal RNA

The stain intensity of the nucleolus organizer regions (NORs) of acrocentric chromosomes was correlated positively with incorporation of [3H]uridine into 18S rRNA and 28S rRNA from cultured diploid human skin fibroblasts. An analysis of these data from twins by a path model indicated that no other common genetic or environmental parameters were required to explain the relationship between NOR scores and uptake of [3H]uridine into mature rRNA species.

Ribosomal 5S genes in relation to C-value in amphibians

We have measured the amount of 5S-ribosomal DNA in the genomes of Xenopus laevis, Triturus cristatus carnifex and Ambystoma mexicanum, three species of Amphibians which have widely different C-values. Our best estimate is that these organisms have about 24,000, 32,000 and 61,000 5S-genes per haploid genome respectively. A trend to increasing 5S gene copynumber with increasing C-values in amphibians is apparent, probably linked to the need to supply more ribosomes to the larger cells which are associated with larger genomes, particularly during the critical phases of oogenesis and embryonic cleavage. The correlation between the two is poor however, and whilst C-value may determine a minimum gene copy-number, there appears to be little constraint on exceeding this minimum in some species. Certain problems encountered in measuring gene copy-numbers, i.e. the criterion dependance of such numbers and the effect of having pseudogenes, are highlighted.

Ribosomal RNA gene number and sequence divergence in the diploid-tetraploid species pair of North American hylid tree frogs

Hyla chrysoscelis (2n = 24) and H. versicolor (2n = 48) are a diploid-tetraploid species pair of tree frogs. Hybridization saturation of isolated 125I-labeled ribosomal RNAs (rRNAs) with filter-immobilized DNA shows that there are twice as many rRNA genes in the tetraploid as in the diploid. For the diploid, saturation occurs at 0.037%, from which it is calculated that there are about 618 copies of the (18 S + 28 S) rRNA genes per haploid genome. Analysis of the extent of hybridization and also the thermal stability of homologous and heterologous hybrids shows that considerably more base substitutions have occurred in the tetraploid rDNA genes than in the diploid since their divergence. This is interpreted to reflect either a relaxation of the gene regulatory "correction" mechanism hypothesized to be responsible for the maintenance of identical tandem rRNA genes in the tetraploid or a release of one gene set from the normal selective constraints.

Regular arrangement of nucleosomes on 5S rRNA genes in Xenopus laevis

The chromatin structure of the oocyte-type 5S RNA genes in Xenopus laevis was investigated. Blot hybridization analysis of DNA from micrococcal nuclease digests of erythrocyte nuclei showed that 5S DNA has the same average nucleosome repeat length, 192 +/- 4 base pairs, as two Xenopus satellite DNAs and bulk erythrocyte chromatin. The positions of nuclease-sensitive regions in the 5S DNA repeats of purified DNA and chromatin from erythrocytes were mapped by using an indirect end-labeling technique. Although most of the sites cleaved in purified DNA were also cleaved in chromatin, the patterns of intensities were strikingly different in the two cases. In 5S chromatin, three nuclease-sensitive regions were spaced approximately a nucleosome length apart, suggesting a single, regular arrangement of nucleosomes on most of the 5S DNA repeats. The observed nucleosome locations are discussed with respect to nucleotide sequences known to be important for expression of 5S RNA. Because the preferred locations appear to be reestablished in each repeating unit, despite spacer length heterogeneity, we suggest that the regular chromatin structure reflects the presence of a sequence-specific DNA-binding component on inactive 5S RNA genes.

Determination of the rate of rRNA synthesis in Xenopus laevis triploid embryos produced by low-temperature treatment

Triploid embryos of Xenopus laevis were obtained by cold-temperature shocking of the fertilized eggs, and the rate of the ribosomal RNA (rRNA) synthesis was determined for comparison with that in diploid embryos. For this purpose, both triploid and diploid embryos were dissociated into cells at the neurula stage, and then labeled with (3H)uridine for varying lengths of time. The rate of rRNA synthesis, as estimated after determination of (3H)UTP specific radioactivity and the total label incorporation into the purified rRNA, was about 0.1 pg/cell/hr for both diploid and triploid embryo cells. Nuclei of triploid embryo cells contained three nucleoli of apparently similar sizes--an indication of the functioning of all the three rRNA gene clusters to a more or less similar extent. Also, rates of synthesis of 4S RNA and 5S RNA were determined: Both rates did not change appreciably between triploid and diploid embryo cells. Based on these results, it appears that transcription of these redundant genes occurs at a constant rate on a per cell basis irrespective of the presence of 1.5 times as many genes as the control.

Ribosomal RNA sequence conservation and gene number in the larval brine shrimp

The haploid genome size of Artemia is determined to be about 0.9 X 10(12), as evidenced both by Feulgen microspectrophotometry of individual diploid class nuclei, which are but one of five polyploid classes present within the larvae, and by analysis of the reassociation kinetics of the isolated single copy DNA component. Polysomes isolated from 24-h incubation stage larvae contain an average of 10 ribosomes per messenger RNA molecule. Their rRNAs are found to have sedimentation coefficients of 18 S and 26 S, corresponding to molecular weights of 0.70 X 10(6) and 1.40 X 10(6), respectively, as determined by polyacrylamide electrophoresis and also by sucrose density centrifugation. Denaturation in glyoxal followed by agarose gel electrophoresis shows that unlike deuterostome rRNAs, Artemia 26 S rRNA contains a cryptic nick about midway in the molecule, which is not found in the 18 S molecule. Isolated rRNAs were labelled in vitro with 125I and hybridized with filter-immobilized DNA to saturation, which occurred at 0.051% for Xenopus, and at 0.074% for Artemia. From these results, it is calculated that in the haploid Artemia genome there are about 320 copies of the (18 S + 26 S) ribosomal RNA genes. Reciprocal heterologous hybridizations between these two species show that they share about 30% homology between their rDNA coding sequences.

Transcription of Xenopus 5S ribosomal RNA genes

The accurate transcription of 5S RNA genes when injected into the nucleus of Xenopus oocytes or when added to an in vitro transcription system has allowed identification of the DNA sequences and one of the protein factors required for 5S RNA synthesis. Moreover, 5S RNA genes as part of intact chromosomes maintain a transcriptionally regulated state when injected into Xenopus oocyte nuclei. A detailed picture of the developmental regulation of 5S RNA gene expression is now emerging.

5S ribosomal RNA genes of the newt Notophthalmus viridescens

The genes which code for the 5S ribosomal RNA in the newt, Notophthalmus viridescens have been cloned and analyzed. Two types of repeating unit were detected: a major type consisting of a 120 bp coding region with a 111 bp spacer, and a minor type composed of a coding region, a pseudogene, and a 113 bp spacer. The pseudogene is a 36 bp segment which corresponds to the 3' terminal third of the 5S RNA gene, and is situated immediately 3' to the gene, being separated from it by 2 bp. Two recombinant plasmids were obtained in which the major and minor units were arranged in an interspersed pattern.

Sequence arrangement of the rRNA genes of the dipteran Sarcophaga bullata

Velocity sedimentation studies of RNA of Sarcophaga bullata show that the major rRNA species have sedimentation values of 26S and 18S. Analysis of the rRNA under denaturing conditions indicates that there is a hidden break centrally located in the 26S rRNA species. Saturation hybridization studies using total genomic DNA and rRNA show that 0.08% of the nuclear DNA is occupied by rRNA coding sequences and that the average repetition frequency of these coding sequences is approximately 144. The arrangement of the rRNA genes and their spacer sequences on long strands of purified rDNA was determined by the examination of the structure of rRNa:DNA hybrids in the electron microscope. Long DNA strands contain several gene sets (18S + 26S) with one repeat unit containing the following sequences in order given: (a) An 18S gene of length 2.12 kb, (b) an internal transcribed spacer of length 2.01 kb, which contains a short sequence that may code for a 5.8S rRNA, (c) A 26S gene of length 4.06 kb which, in 20% of the cases, contains an intron with an average length of 5.62 kb, and (d) an external spacer of average length of 9.23 kb.

Gene expression in eukaryotes

Gene expression in eukaryotes is influenced by a wide variety of mechanisms including the loss, amplification, and rearrangement of genes. Genes are differentially transcribed, and the RNA transcripts are variably utilized. Multigene families regulate the amount, the diversity, and the timing of gene expression. The present level of understanding of gene expression in eukaryotes is attributable mainly to biochemical methods rather than to traditional genetics. The new techniques that permit analysis and modification of purified genes of known function will identify both the control regions in eukaryotic genes as well as the molecules within cell that influence gene expression.

The reactivation of developmentally inert 5S genes in somatic nuclei injected into Xenopus oocytes

In the frog Xenopus, the somatic-type 5S ribosomal RNA genes are active in all cells; the oocyte-type 5S genes are active in oocytes but not in somatic cells. A new method of native gel electrophoresis resolves the two types of 5S RNA which are of the same length but different sequence. When somatic nuclei were injected into oocytes, their inactive oocyte-type 5S genes often remained inactive, and had thus conserved their developmentally regulated condition. Other conditions, which include treatment with 0.35 M NaCl, reactivated the genes.