Structural organization of rat ribosomal genes restriction endonuclease analysis of genomic and cloned ribosomal DNAs

Expression of the specific type IV phosphodiesterase gene PDE4B3 during different phases of long-term potentiation in single hippocampal slices of rats in vitro

Hippocampal long-term potentiation (LTP), the most prominent cellular model for learning and memory formation, consists of phases: early-LTP (<4 h) and late-LTP (>4 h), with the latter dependent upon protein translation and transcription. To explore the molecular processes that might be specifically regulated during late-LTP, we have modified standard electrophysiological and molecular biological methods, which allowed the cloning of activated genes and their products from single hippocampal slices in vitro 8 h after LTP induction. From one such screen we identified a specific type IV phosphodiesterase gene, PDE4B3, the first cAMP-specific phosphodiesterase to be associated with LTP. Previous studies documented an integral role for the cAMP-PKA system in late-LTP and recently, inhibition of cAMP degradation facilitates LTP and ameliorates mnemonic deficits. We now report that PDE4B3 is modulated during LTP phases. Its activation is NMDA-receptor dependent and its transcription is transiently up-regulated 2 h after tetanization. Protein expression peaks 6 h after LTP induction and is rapidly down-regulated at 8 h, whereas cAMP levels decrease during LTP phases. Immunohistochemical studies identified that the majority of type IV phosphodiesterase protein staining is localized to the cell bodies and dendrites of neurones in hippocampal CA1.

Mapping the sites of initiation of DNA replication in rat and human rRNA genes

To study the organization of DNA replication in mammalian rRNA genes, the sites of initiation of DNA synthesis in rat and human rRNA genes were mapped by two independent techniques. In rat cells the growth of the nascent DNA chains was blocked by Trioxsalen cross-links introduced in vivo. The fraction of "restricted" nascent DNA chains labeled in vivo was isolated, and the abundance in this fraction of cloned ribosomal DNA sequences was determined by hybridization. In the experiments with human cells, the nascent DNA chains were allowed to grow unrestricted for a certain period of time and the movement of the replication forks along the rRNA genes was followed by hybridization of cloned ribosomal DNA sequences to the "unrestricted" nascent DNA fragments fractionated according to size. The results show that in both rRNA genes there are two well defined regions of initiation of DNA synthesis. The first one is located upstream of the transcription units and the second one is located at the 3'-end of the coding regions of the ribosomal DNA repeats.

Fragments of rDNA within the Chinese hamster genome

We report the isolation and partial characterization of distinct EcoRI fragments of the Chinese hamster genome which contain regions complementary to a 1-kb portion of the mature 18 S ribosomal RNA molecule. This previously undescribed 18 S rDNA-like region, which we have termed a "fragment of ribosomal DNA" (frDNA), has been shown by sequence analysis to correspond to a region extending 1 kb upstream from the 3' terminus of the mature 18 S rRNA. Within the five frDNA-containing clones described here, no other region of the ribosomal RNA cistron was detected, making it unlikely that these are polymorphic forms of the ribosomal DNA repeat. The 18 S rDNA-complementary region appears to be flanked by an imperfect direct repeat, which could have been the result of the retroinsertion of a fragment of ribosomal RNA. Directly adjacent to the 18 S rDNA-like region we have identified nonribosomal sequences which appear common to all of the frDNA-containing clones we examined. At least eight different-sized EcoRI fragments contain frDNAs and the abundance of the frDNAs appears to be of the order of 30 per genome. The occurrence of multiple copies of this ribosomal-nonribosomal chimera suggests that, once formed, the chimera was duplicated within the genome.

Evolutionary changes of sequences and factors that direct transcription termination of human and mouse ribsomal genes

We have analyzed the sequences required for termination of human rDNA transcription. The human ribosomal transcription unit is shown to extend about 350 nucleotides into the 3'-terminal spacer and ends immediately upstream of a region with a distinct sequence heterogeneity. This heterogeneous region contains a cluster of conserved 10-base pair sequence elements which exert a striking homology to the proximal part of the 18-base pair murine rDNA transcription termination signal sequence, termed SalI box. Exonuclease III protection assays and in vitro transcription experiments with both homologous and heterologous human-mouse minigene constructs, and extracts from HeLa or Ehrlich ascites cells, reveal a functional analogy of the human sequence to the mouse SalI box. It mediates binding of a nuclear protein which functions as a transcription termination factor. The murine signal sequence is recognized by the human factor but not vice versa. The different sequence specificities and electrophoretic properties of the functionally equivalent protein factors suggest that a molecular coevolution has taken place between the termination signal sequences and the genes coding for the termination factors.

Evolutionary changes of sequences and factors that direct transcription termination of human and mouse ribsomal genes

We have analyzed the sequences required for termination of human rDNA transcription. The human ribosomal transcription unit is shown to extend about 350 nucleotides into the 3'-terminal spacer and ends immediately upstream of a region with a distinct sequence heterogeneity. This heterogeneous region contains a cluster of conserved 10-base pair sequence elements which exert a striking homology to the proximal part of the 18-base pair murine rDNA transcription termination signal sequence, termed SalI box. Exonuclease III protection assays and in vitro transcription experiments with both homologous and heterologous human-mouse minigene constructs, and extracts from HeLa or Ehrlich ascites cells, reveal a functional analogy of the human sequence to the mouse SalI box. It mediates binding of a nuclear protein which functions as a transcription termination factor. The murine signal sequence is recognized by the human factor but not vice versa. The different sequence specificities and electrophoretic properties of the functionally equivalent protein factors suggest that a molecular coevolution has taken place between the termination signal sequences and the genes coding for the termination factors.

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.

Nucleotide sequence analysis of the spacer regions flanking the rat rRNA transcription unit and identification of repetitive elements

We investigated the organization of the rat rDNA non-transcribed spacer (NTS) by determining the sequence of large NTS segments located upstream (2501 bp) and downstream (4025 bp) from the rRNA transcription unit. We identified four B2-like and two ID mobile elements. They may be grouped in three pairs with the members of each pair located in the upstream and downstream NTS. The ID sequences are identical to the consensus sequence, while the pairs of B2-like elements show 85% and 50/65% homology to the consensus B2 sequence. The proximal part of the downstream NTS contains a region of widely diverged SalI tandem repeats. A considerable part of the analyzed upstream and downstream NTS sequences is constituted by different types of simple sequences and long poly(purine) X poly(pyrimidine) tracts. These data show that the rat rDNA NTS regions flanking the rRNA transcription unit are characterized by a combination of short interspersed (B2-superfamily) and various simple sequences.

Characterization of rat ribosomal DNA II. identification of the highly repetitive DNA in the 3' non-transcribed spacer

The nucleotide sequence of one of the non-transcribed spacer subclones, p1.7, from the region 3' to rat 45 S pre-rRNA has been determined. Within 1612 base-pairs, the fragment contains two distinct regions of highly repetitive DNA, one of which can serve as a site for initiation in vitro by RNA polymerase III. The first is the alternating purine-pyrimidine sequence (A-C)21. The second of these regions has 95% homology to the identifier sequence and served as the template for RNA polymerase III transcription in vitro. The in vitro polymerase III template is aligned in opposite polarity to the direction of transcription of 45 S rRNA. Located near the identifier sequence is a region that is 59% homologous to the type-II Alu sequences. It would seem, therefore, that members of more than one highly repetitive sequence family have accumulated in the non-transcribed spacers. These data also suggest that within the non-transcribed spacers these families have evolved (sequence variation) at different rates, until one of them, the Alu type-II-like element, may represent a new Alu type-II subfamily.

Molecular analysis of the heterogeneity region of the human ribosomal spacer

The human ribosomal non-transcribed spacers are 30 X 10(3) base-pairs (or 30 kb) in length with a limited length heterogeneity localized in a specific region downstream from the 3' end of the transcribed region. Total DNA digested with EcoRI and BamHI and hybridized with a probe containing the 3' end of the 28 S ribosomal RNA coding region shows four major bands of 3.9 kb, 4.6 kb, 5.4 kb and 6.2 kb. The 5.4 kb band is the most abundant in every individual, followed by the 4.6 kb band. The longest and the shortest size classes are less well-represented and may even be absent. Every individual shows his own pattern of relative abundance of non-transcribed spacer length classes that can be followed through generations. We decided to investigate the molecular structure of the heterogeneity region, in order to cast light onto the mechanisms underlying the origin and maintenance of this length heterogeneity. Pertinent spacer regions of eight ribosomal clones from two human genomic libraries were subcloned and analyzed by restriction mapping and nucleotide sequencing. In the minimal length class, there is a sequence of 700 base-pairs that appears to be tandemly duplicated once, twice or three times in the other length classes. This repeated DNA module contains a region consisting of repetitions of simple pyrimidine groups like C-T, C-T-T-T or C-C-C-T. DNA module repeats may differ by the length of this pyrimidine-rich region. However, these length variations are not continuous, as revealed by Southern transfer analysis of several individuals and different cloned gene units: instead, the repeated modules fall into two discrete length classes of about 700 base-pairs and 800 base-pairs. An imperfect duplication of a short sequence of 86/89 base-pairs is present at the boundary between the heterogeneity region and the upstream flanking region, representing a very ancient duplication event.

Nucleotide sequence of a complete ribosomal spacer of D. melanogaster

We determined the nucleotide sequence of a D. melanogaster ribosomal DNA spacer. Sequences of various portions of different cloned ribosomal spacers have been previously reported. We extend the analysis to cover the entire nontranscribed and external transcribed regions. Comparison to other cloned ribosomal DNA gene units of this species confirms a conserved general organization of the ribosomal spacer through different size classes. D. melanogaster ribosomal gene units interrupted by insertions are known to be transcribed at a much lower level than the continuous gene units. Nonetheless previous sequence analysis of a region around the transcription initiation site did not reveal significant differences in rDNA genes with and without insertions. We extend such analysis to cover the last two promoter duplications in the spacer and the entire external transcribed spacer up to the 5' cleavage site of the 18S rRNA.

Structural organization of rat ribosomal RNA genes: interspersed sequences and their putative role in the alignment of nucleosomes

We have observed four regions containing highly repetitive interspersed sequences in the nontranscribed spacer (NTS) of the rat rRNA genes. Two of them (A and B) are located at a distance of 3-5 kb upstream from the transcription start point and two others (C and D) at a distance of 2-5 kb downstream from the 3' end of the 28S rRNA gene. These repetitive sequences are widely dispersed in the genome and are included both in small-copy regions and in the families of extended reiterated sequences. The sequences of three fragments were determined: one from the C2 region, 1100 bp in length and two from A and C1 regions, 110-120 bp long. These regions are characterized by the presence of 'simple' sequences, such as (AC)n, (ACC)n, (GAG)n, (GGGA)n, (TAAG)n, and also of long blocks, (G)n and (A)n. In the C2 region two palindromes, 16 and 14 nt long, were found, one of them including a XhoI site. Mobile element B2 was observed in regions B and C. All four regions, A, B, C and D, contain sets of simple sequences, among which some common elements have been found. Theoretical prediction of the nucleosomal disposition in the C region indicates that the combination of simple sequences existing in the given area secures fixed positions of the nucleosomes, one of the nucleosomes being formed on the B2 element. Moreover, a striking periodicity, with the repeat length close to that of the rat nucleosomal DNA, has been observed. A hypothesis is put forward that the simple sequences can dictate the location of nucleosomes on the adjoining DNA sequences, thereby regulating the gene activity.

Excess 5'-terminal sequences in the rat nucleolar 28S ribosomal RNA

The 5'-termini of purified rat liver nucleolar and cytoplasmic 28S ribosomal RNA (rRNA) are precisely located within the homologous rDNA sequence by S1 nuclease protection mapping using an appropriate rDNA restriction fragment. The 5'-termini of nucleolar 28S rRNA are heterogeneous in length. The bulk of the nucleolar 28S rRNA map within two CTC motifs in rDNA located in the internal transcribed spacer 2 at the 50-60 and 5-15 bp upstream from the site of the homogeneous 5'-terminus of the cytoplasmic 28S rRNA. These results provide direct proof that nucleolar 28S rRNA molecules contain excess sequences at their 5'-termini and require further processing to generate the mature cytoplasmic 28S rRNA.

Mapping of the major early endonuclease cleavage site of the rat precursor to rRNA within the internal transcribed spacer sequence of rDNA

The endonuclease cleavage of 41 S pre-rRNA to yield 32 S and 21 S pre-rRNA constitutes a major early step in the processing of pre-rRNA in rat liver. The 5'-terminus of 32 S pre-rRNA and the 3'-terminus of 21 S pre-rRNA were precisely located within the rDNA sequence by S1 nuclease protection mapping and use of appropriate rDNA restriction fragments. The 5'-terminus of 12 S pre-rRNA, an initial product of 32 S pre-rRNA processing, was also mapped within the rDNA sequence. The 5'-termini of 32 S and 12 S pre-rRNA coincide and map within a 14-residue T-tract (non-coding strand) at 161-163 bp upstream from the 5'-end of the 5.8 S rRNA gene. The 3'-terminus of 21 S pre-rRNA maps within the same T-tract. These results show that the endonuclease cleavage occurs within a U-tract in the internal transcribed spacer 1 sequence of 41 S pre-rRNA. The homogeneity of the 5'- or 3'-termini of 32 S, 12 S and 21 S pre-rRNA indicates also that the terminal processing of these molecules, if any, is markedly slower. The coincidence in the location of 32 S and 12 S pre-rRNA 5'-termini shows further that the endonuclease cleavage of 32 S pre-rRNA precedes the removal of its 5'-terminal segment to yield 5.8 S rRNA. The absence in the whole pre-rRNA internal transcribed spacer of sequences complementary to the target U-tract suggests that the endonuclease cleavage, generating 32 S and 21 S pre-rRNA, occurs in a single-stranded loop of U-residues.

Localization and structure of endonuclease cleavage sites involved in the processing of the rat 32S precursor to ribosomal RNA

The initial endonuclease cleavage site in 32 S pre-rRNA (precursor to rRNA) is located within the rate rDNA sequence by S1-nuclease protection mapping of purified nucleolar 28 S rRNA and 12 S pre-rRNA. The heterogeneous 5'- and 3'-termini of these rRNA abut and map within two CTC motifs in tSi2 (internal transcribed spacer 2) located at 50-65 and 4-20 base-pairs upstream from the homogeneous 5'-end of the 28 S rRNA gene. These results show that multiple endonuclease cleavages occur at CUC sites in tSi2 to generate 28 S rRNA and 12 S pre-rRNA with heterogeneous 5'- and 3'-termini, respectively. These molecules have to be processed further to yield mature 28 S and 5.8 S rRNA. Thermal-denaturation studies revealed that the base-pairing association in the 12 S pre-rRNA:28 S rRNA complex is markedly stronger than that in the 5.8 S:28 S rRNA complex. The sequence of about one-quarter (1322 base-pairs) of the 5'-part of the rat 28 S rDNA was determined. A computer search reveals the possibility that the cleavage sites in the CUC motifs are single-stranded, flanked by strongly base-paired GC tracts, involving tSi2 and 28 S rRNA sequences. The subsequent nuclease cleavages, generating the termini of mature rRNA, seem to be directed by secondary-structure interactions between 5.8 S and 28 S rRNA segments in pre-rRNA. An analysis for base-pairing among evolutionarily conserved sequences in 32 S pre-rRNA suggests that the cleavages yielding mature 5.8 S and 28 S rRNA are directed by base-pairing between (i) the 3'-terminus of 5.8 S rRNA and the 5'-terminus of 28 S rRNA and (ii) the 5'-terminus of 5.8 S rRNA and internal sequences in domain I of 28 S rRNA. A general model for primary- and secondary-structure interactions in pre-rRNA processing is proposed, and its implications for ribosome biogenesis in eukaryotes are briefly discussed.

Primary and secondary structure of rat 28 S ribosomal RNA

The primary structure of rat (Rattus norvegicus) 28 S rRNA is determined inferred from the sequence of cloned rDNA fragments. The rat 28 S rRNA contains 4802 nucleotides and has an estimated relative molecular mass (Mr, Na-salt) of 1.66 X 10(6). Several regions of high sequence homology with S. cerevisiae 25 S rRNA are present. These regions can be folded in characteristic base-paired structures homologous to those proposed for Saccharomyces and E. coli. The excess of about 1400 nucleotides in the rat 28 S rRNA (as compared to Saccharomyces 25 S rRNA) is accounted for mainly by the presence of eight distinct G+C-rich segments of different length inserted within the regions of high sequence homology. The G+C content of the four insertions, containing more than 200 nucleotides, is in the range of 78 to 85 percent. All G+C-rich segments appear to form strongly base-paired structures. The two largest G+C-rich segments (about 760 and 560 nucleotides, respectively) are located near the 5'-end and in the middle of the 28 S rRNA molecule. These two segments can be folded into long base-paired structures, corresponding to the ones observed previously by electron microscopy of partly denatured 28 S rRNA molecules.

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.

Genomic organization of rat rDNA

A detailed restriction map was determined for a 10.9 KB region that contains the initiation site for 45S pre-rRNA and the first 1.7 KB of the 18S rRNA coding region. When the restriction pattern of the cloned rDNA was compared with that of total rat DNA, the rDNA regions of both Sprague-Dawley and BD-9 rats were identical to each other and to that of the cloned rDNA. However, both strains exhibit a major polymorphism consisting of an insertion of 0.9 KB of DNA in the nontranscribed spacer between 0.29 KB and 1.8 KB upstream from the 45S RNA initiation site. This region consists of tandem repeats approximately 130 base pairs in length. These repeats contain large poly T tracts and are similar in sequence to analogous elements 5' to the origin of mouse rRNA transcription. Regions containing highly repetitious DNA sequences were located at sites 2.8 KB and 4.3 KB upstream from the initiation site. The repetitive sequence at 2.8 KB from the initiation site anneal to a known Alu-equivalent type 2 sequence derived from the second intron of the rat growth hormone gene.