Nucleotide sequence of an external transcribed spacer in Xenopus laevis rDNA: sequences flanking the 5' and 3' ends of 18S rRNA are non-complementary

Sequence analysis of the ribosomal DNA internal transcribed spacer region in some scallop species (Mollusca: Bivalvia: Pectinidae)

The internal transcribed spacer (ITS) region of the ribosomal DNA from the European scallops Aequipecten opercularis, Mimachlamys varia, Hinnites distortus, and Pecten maximus was PCR amplified and sequenced. For each species, three or five clones were examined. The size ranged between 636 and 713 bp (ITS1, 209-276 bp; 5.8S rRNA gene, 157 bp; ITS2, 270-294 bp) and GC content ranged between 47 and 50% (ITS1, 43-49%; 5.8S rRNA gene, 56-57%; ITS2, 44-49%). Variation within repeats was minimal; only clones from M. varia and P. maximus displayed a few variable sites in ITS2. Among scallops, including Chlamys farreri whose ITS sequence appears in databases, significant variation was observed in both ITS1 and ITS2. Phylogenetic analysis using ITS1, ITS2, or both spacer sequences always yielded trees with similar topology. Aequipecten opercularis and P. maximus grouped in one clade and the other three scallops (C. farreri, M. varia, and H. distortus) in another, where M. varia and H. distortus are the more closely related species. These results provide new insights into the evolutionary relationships of scallop species and corroborate the close evolutionary relationship between the tribes Aequipectinini and Pectinini previously deduced from 18S rDNA sequences.

Analysis of intergenic spacer transcripts suggests 'read-around' transcription of the extrachromosomal circular rDNA in Euglena gracilis

We report here the sequence of the 1743 bp intergenic spacer (IGS) that separates the 3'-end of the large subunit ribosomal RNA (rRNA) gene from the 5'-end of the small subunit (SSU) rRNA gene in the circular, extrachromosomal ribosomal DNA (rDNA) of Euglena gracilis. The IGS contains a 277 nt stretch of sequence that is related to a sequence found in ITS 1, an internal transcribed spacer between the SSU and 5.8S rRNA genes. Primer extension analysis of IGS transcripts identified three abundant reverse transcriptase stops that may be analogous to the transcription initiation site (TIS) and two processing sites (A' and A0) that are found in this region in other eukaryotes. Features that could influence processing at these sites include an imperfect palindrome near site A0 and a sequence near site A' that could potentially base pair with U3 small nucleolar RNA. Our identification of the TIS (verified by mung bean nuclease analysis) is considered tentative because we also detected low-abundance transcripts upstream of this site throughout the entire IGS. This result suggests the possibility of 'read-around' transcription, i.e. transcription that proceeds multiple times around the rDNA circle without termination.

Xenopus borealis and Xenopus laevis 28S ribosomal DNA and the complete 40S ribosomal precursor RNA coding units of both species

We have determined the nucleotide sequence of Xenopus borealis 28S ribosomal DNA (rDNA) and have revised the sequence of Xenopus laevis 28S rDNA (Ware et al., Nucl. Acids Res. 11, 7795-7817 (1983)). In the regions encoding the conserved structural core of 28S rRNA (2490 nucleotides) there are only four differences between the two species, each difference being a base substitution. In the variable regions, also called eukaryotic expansion segments (ca. 1630 nucleotides) there are some 61 differences, due to substitutions, mini-insertions and mini-deletions. Thus, evolutionary divergence in the variable regions has been at least 20-fold more rapid than in the conserved core. A search for intraspecies sequence variation has revealed minimal heterogeneity in X. laevis and none in X. borealis. At three out of four sites where heterogeneity was found in X. laevis (all in variable regions) the minority variant corresponded to the standard form in X. borealis. Intraspecies heterogeneity and interspecies divergence in the 28S variable regions are much less extensive than in the transcribed spacers. The 28S sequences are from the same clones that were used previously for sequencing the 18S genes and transcribed spacers. The complete sequences of the 40S precursor regions of the two reference clones are given.

Preribosomal RNA processing in Xenopus oocytes does not include cleavage within the external transcribed spacer as an early step

Recently it has been reported that U3 snRNA is necessary for: (a) internal cleavage at +651/+657 within the external transcribed spacer (ETS) of mouse precursor ribosomal RNA (pre-rRNA); and (b) cleavage at the 5' end of 5.8S rRNA in Xenopus oocytes. To study if U3 snRNA plays a role at more than one processing site in the same system, we have investigated whether internal cleavage sites exist within the ETS of Xenopus oocyte pre-rRNA. The ETS of Xenopus pre-rRNA contains the consensus sequence for the mammalian early processing site (+651/+657 in mouse pre-rRNA), but freshly prepared RNA from Xenopus oocytes has no cuts in this region. The only putative cleavage sites we found in the ETS of Xenopus oocyte pre-rRNA are a cluster further downstream of the mouse early processing site consensus sequence. This cluster is not homologous to the mouse +651/+657 sites because unlike the latter it is (a) not abolished by disruption of U3 snRNA, (b) not cleaved during early steps of pre-rRNA processing, and (c) lacks sequence similarity to the +651/+657 consensus. Therefore, pre-rRNA of Xenopus oocytes does not cleave within the ETS as an early step in rRNA processing. We conclude that cleavage within the ETS is not an obligatory early step needed for the rest of rRNA maturation.

Secondary structure of the 5' external transcribed spacer of vertebrate pre-rRNA. Presence of phylogenetically conserved features

Eucaryotic pre-rRNA spacers are evolutionarily highly variable in sequence and size, and are markedly expanded in vertebrates, particularly in mammals. The longest mammalian spacer by far is the 3.5-4-kb 5' external transcribed spacer (5'-ETS), which is excised in two steps. We present a folding model for the entire mammalian 5'-ETS, derived from comparative analyses and thermodynamic predictions for mouse, rat and human sequences, which should prove helpful in identifying cis-acting processing signals, particularly those involved in its early internal cleavage, for which U3 RNA is an essential factor. Although the rodent and primate sequences have extensively diverged, a series of relatively conserved sequence tracts can nevertheless be identified: they participate in base-pairing, preserved through the occurrence of compensatory base changes, which delineate four independent domains of secondary structure. The first domain is located entirely upstream from the site of internal cleavage. The second domain, immediately downstream from this cleavage site, encompasses most of the region required for faithful and efficient in vitro processing at this site. Phylogenetically supported conserved structures also define two other independent domains, encompassing most of the 5'-ETS length, with the presence of giant hairpins (extending from the conserved core elements) which exhibit both some analogous features and substantial differences between man and mouse. The comparative analysis was extended to the two other vertebrate sequences available so far, amphibians Xenopus laevis and Xenopus borealis. The amphibian folding model, supported by comparative evidence between these two species, displays some features in common with the mammalian model, with a similar organization into four separate domains of secondary structure, suggesting the functional relevance of these structures in the process of ribosome formation.

GC balance in the internal transcribed spacers ITS 1 and ITS 2 of nuclear ribosomal RNA genes

The internal transcribed spacer (ITS) 1 and 2, the 5.8S rRNA gene, and adjacent 18S rRNA and 25S rRNA coding regions of two Cucurbitaceae (Cucurbita pepo, zucchini, ITS 1: 187 bp, and ITS 2: 252 bp in length, and Cucumis sativus, cucumber, ITS 1: 229 bp, and ITS 2: 245 bp in length) have been sequenced. The evolutionary pattern shown by the ITSs of these plants is different from that found in vertebrates. Deletions, insertions, and base substitutions have occurred in both spacers; however, it is obvious that some selection pressure is responsible for the preservation of stem-loop structures. The dissimilarity of the 5' region of ITS 2 found in higher plants has consequences for proposed models on U3 snRNA-ITS 2 interaction in higher eukaryotes. The two investigated Cucurbitaceae species show a G + C content of ITS 1 that nearly equals that of ITS 2. An analysis of the ITS sequences reveals that in 19 out of 20 organisms published, the G + C content of ITS 1 nearly equals that of ITS 2, although it ranges from 20% to 90% in different organisms (GC balance). Moreover, the balanced G + C content of the ITSs in a given species seems to be similar to that of so-called expansion segments (ESs) in the 25/28S rRNA coding region. Thus, ITSs show a phenomenon called molecular coevolution with respect to each other and to the ESs. In the ITSs of Cucurbitaceae the balanced G + C composition is at least partly achieved by C to T transitions, via deamination of 5-methylcytosine. Other mutational events must be taken into account. The appearance of this phenomenon is discussed in terms of functional constraints linked to the structures of these spacers.

Structure of the 5'-external transcribed spacer of the human ribosomal RNA gene

We report the complete nucleotide sequence of the 3627 bp long 5'-external transcribed spacer (ETS) of a human ribosomal RNA gene. This sequence exhibits only very limited homologies with its mouse counterpart, the only other mammalian specimen analyzed so far. It has very peculiar compositional characteristics, with a highly biased base content (very rich in G + C, very poor in A) and also some very strong dinucleotide preferences. Interestingly, these specific features are shared by the mouse sequence, despite the extensive sequence divergence, and also apply to the other transcribed spacers of mammals indicating that a common and strong structural constraint is exerted on all these regions of the ribosomal gene. An outstanding secondary structure can be formed within the human ETS RNA, which could have a significant role in preribosome assembly.

Characterization of the TMV encapsidation initiation site on 18S rRNA

Tobacco Mosaic Virus capsid protein oligomers react with and encapsidate 18S rRNA from both plant and mammalian sources in vitro. The site (ei) in 18S rRNA which reacts with capsid protein to initiate the packaging reaction has been localized and partially characterized by testing the ability of transcripts from different regions of a cloned Cucurbita pepo rDNA repeat unit to become encapsidated. The 18S rRNA ei is found to react more slowly with capsid protein than does the functional virion ei and to lie within a 43 nucleotide region which starts at position 157 from the 5' terminus of 18S rRNA. When 6 nucleotides are removed from the 5' end, the remaining 37 nucleotide segment is still reactive, but with reduced efficiency. The primary structure of the reactive segment has limited similarity to the virion ei and can be folded into a stem-loop. The first 18 nucleotides of the ei region is highly conserved from an evolutionary standpoint and this may account for the ability of 18S rRNAs from both plant and mammalian sources to be encapsidated.

Sequence and secondary structure of the 5' external transcribed spacer of mouse pre-rRNA

We report the sequence of the 4006-nucleotide 5' external transcribed spacer (5'ETS) of the mouse ribosomal primary transcript. These data complete the sequence of the 13.4-kb mouse rRNA gene, thus providing a mammalian rRNA gene structure, in addition to yeast and Xenopus. The mouse 5'ETS displays a highly biased base content (very high in GC and particularly low in A), closely similar to the other transcribed spacers of the mouse ribosomal gene. This region seems to have accumulated sequence variation relatively rapidly during vertebrate evolution, with the possible insertion in rodents of sequences structurally similar to retroposons. About half the length of the mouse 5'ETS can fold into a giant and highly stable secondary structure, which is probably evolutionarily conserved in mammals and which could play an important role in the higher-order organization of mammalian pre-ribosomes.

Nucleotide sequence determination and secondary structure of Xenopus U3 snRNA

Using a combination of RNA sequencing and construction of cDNA clones followed by DNA sequencing, we have determined the primary nucleotide sequence of U3 snRNA in Xenopus laevis and Xenopus borealis. This molecule has a length of 219 nucleotides. Alignment of the Xenopus sequences with U3 snRNA sequences from other organisms reveals three evolutionarily conserved blocks. We have probed the secondary structure of U3 snRNA in intact Xenopus laevis nuclei using single-strand specific chemical reagents; primer extension was used to map the positions of chemical modification. The three blocks of conserved sequences fall within single-stranded regions, and are therefore accessible for interaction with other molecules. Models of U3 snRNA function are discussed in light of these data.

Structural analysis of the human U3 ribonucleoprotein particle reveal a conserved sequence available for base pairing with pre-rRNA

The human U3 ribonucleoprotein (RNP) has been analyzed to determine its protein constituents, sites of protein-RNA interaction, and RNA secondary structure. By using anti-U3 RNP antibodies and extracts prepared from HeLa cells labeled in vivo, the RNP was found to contain four nonphosphorylated proteins of 36, 30, 13, and 12.5 kilodaltons and two phosphorylated proteins of 74 and 59 kilodaltons. U3 nucleotides 72-90, 106-121, 154-166, and 190-217 must contain sites that interact with proteins since these regions are immunoprecipitated after treatment of the RNP with RNase A or T1. The secondary structure was probed with specific nucleases and by chemical modification with single-strand-specific reagents that block subsequent reverse transcription. Regions that are single stranded (and therefore potentially able to interact with a substrate RNA) include an evolutionarily conserved sequence at nucleotides 104-112 and nonconserved sequences at nucleotides 65-74, 80-84, and 88-93. Nucleotides 159-168 do not appear to be highly accessible, thus making it unlikely that this U3 sequence base pairs with sequences near the 5.8S rRNA-internal transcribed spacer II junction, as previously proposed. Alternative functions of the U3 RNP are discussed, including the possibility that U3 may participate in a processing event near the 3' end of 28S rRNA.

Structural analysis of the human U3 ribonucleoprotein particle reveal a conserved sequence available for base pairing with pre-rRNA

The human U3 ribonucleoprotein (RNP) has been analyzed to determine its protein constituents, sites of protein-RNA interaction, and RNA secondary structure. By using anti-U3 RNP antibodies and extracts prepared from HeLa cells labeled in vivo, the RNP was found to contain four nonphosphorylated proteins of 36, 30, 13, and 12.5 kilodaltons and two phosphorylated proteins of 74 and 59 kilodaltons. U3 nucleotides 72-90, 106-121, 154-166, and 190-217 must contain sites that interact with proteins since these regions are immunoprecipitated after treatment of the RNP with RNase A or T1. The secondary structure was probed with specific nucleases and by chemical modification with single-strand-specific reagents that block subsequent reverse transcription. Regions that are single stranded (and therefore potentially able to interact with a substrate RNA) include an evolutionarily conserved sequence at nucleotides 104-112 and nonconserved sequences at nucleotides 65-74, 80-84, and 88-93. Nucleotides 159-168 do not appear to be highly accessible, thus making it unlikely that this U3 sequence base pairs with sequences near the 5.8S rRNA-internal transcribed spacer II junction, as previously proposed. Alternative functions of the U3 RNP are discussed, including the possibility that U3 may participate in a processing event near the 3' end of 28S rRNA.

In vivo transcription from multiple spacer rRNA gene promoters during early development and evolution of the intergenic spacer in the brine shrimp Artemia

The control of ribosomal RNA (rRNA) gene expression during development can be productively studied by examination of the relationship between promoter structure and function as well as the processing of primary transcripts. Toward this end total cell RNA was extracted from embryos at various stages and probed with cloned rRNA genes using the "dot blot" method. This exercise showed that rRNA gene expression is a stage-specific process and is thus under developmental control. S1 nuclease protection experiments localized fourteen different upstream DNA sites encoding 5'-termini of pre-rRNAs during this synthetic phase of development. There is no indication of any spacer fail-safe terminator function. The S1 approach contributed to the sequencing of several of the sites. Comparative sequence alignments reveal short conserved regions in DNAs corresponding to these sites, which are shown to fall into two structural classes. Sites 3, 4, 6 and 9 are proposed to function in transcription initiation and are found to have the consensus sequence 5'...T-A-T-A-T-Pu-Pu-Pu-G-Pu-Pu-G-T-C-A 3'. Sites 1, 2, 5 and 8 which are proposed to function in 5'-processing have the consensus sequence; 5'...Pu-G-T-Pu-T-T-G 3'. These short sequence conserved regions are hypothesized to serve as recognition signals for proteins within the rDNA transcription initiation complex and for 5'-processing enzymes, respectively. Sequencing of the intergenic spacer region from which a model for spacer evolution is derived shows that tandem ca 600 bp subrepeats explain much of the multiplicity observed within control sites.

Structure of the Bombyx mori rDNA: initiation site for its transcription

The initiation site of rDNA transcription in Bombyx mori was determined to be located at 909bp upstream from the 5'- end of mature 18s rRNA by S1-nuclease mapping and primer extension experiment. An in vitro transcription system, which was constructed using posterior silk glands of Bombyx larvae, initiated the transcription of cloned rDNA at exactly the same site as determined for the in vivo transcription above. The primary transcript seemed to be processed at about 200b downstream of the initiation site both in vivo and in vitro. Sequence analyses of the flanking region of the initiation site revealed that short repetitive sequences are widely distributed throughout the NTS region, and that a highly AT-rich region resides immediately upstream of the initiation region.

Identification of the locations of the methyl groups in 18 S ribosomal RNA from Xenopus laevis and man

The 18 S ribosomal RNA from a variety of vertebrate species contains some 40 to 47 methyl groups. The majority of these are 2'-O-ribose substituents; the remaining few are on bases. Several lines of evidence have permitted the identification of the precise locations of the methyl groups in the primary structure of 18 S ribosomal RNA of Xenopus laevis and man. Digestion of RNA with T1 ribonuclease, followed by analysis of the methylated oligonucleotides yielded data on sequences immediately surrounding the methyl groups. Preparative hybridization of X. laevis 18 S ribosomal RNA restriction fragments of ribosomal DNA, followed by fingerprinting analysis on RNA recovered from the hybrids, allowed each methylated oligonucleotide to be mapped to a specific region within 18 S ribosomal RNA. The data on RNA oligonucleotides were correlated with Xenopus ribosomal DNA sequence data in the regions defined by the mapping experiments to identify the precise locations of most of the methyl groups in the X. laevis 18 S RNA sequence. The remaining uncertainties in Xenopus were solved with the aid of data from ribonuclease A fingerprints and, in a few instances, relevant oligonucleotide or sequence data from other laboratories. The locations of most of the methyl groups in human 18 S ribosomal RNA were deduced from the high degree of correspondence between methylated oligonucleotides from human and X. laevis 18 S RNA, together with knowledge of the human 18 S ribosomal DNA sequence. The remaining methylation sites in human 18 S RNA were located with assistance from relevant published comparative data. In the aligned sequences, human and other mammalian 18 S RNA are methylated at all the same positions as in X. laevis, and there are seven additional 2'-O-methylation sites in mammalian 18 S RNA. Further features of the methyl group distribution are briefly reviewed.

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.

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.

Processing of the large rRNA precursor: two proposed categories of RNA-RNA interactions in eukaryotes

The 5.8S RNA gene of eukaryotes is separated from the 26-28S rRNA gene by the internal transcribed spacer 2 (ITS 2). A compilation of known ITS 2 sequences is presented here. Four characteristic features of the ITS 2 primary structure are shared by all vertebrates. In contrast, lower eukaryotes lack most of these features, suggesting that the excision of the ITS 2 transcript during processing may differ between vertebrates and lower eukaryotes. Since the transcripts of rRNA ITS 2 and mRNA introns share some similarity, analogies have been made between the mechanisms of their removal during RNA maturation. A model is proposed for hydrogen-bonding of U3 snRNA with the 5' end of the vertebrate ITS 2 transcript. This U3 snRNA-ITS 2 RNA interaction does not appear to be used in ITS 2 processing in lower eukaryotes. Instead, in lower eukaryotes a region within the ITS 2 itself has the potential to hydrogen-bond to the 5' end of the ITS 2 transcript.

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.

5'-Cleavage site of D. melanogaster 18 S rRNA

We determined the nucleotide sequence of the DNA region around the 5'-terminus of 18 S rRNA in two cloned rDNA gene units of Drosophila melanogaster. The 5'-base is within a sequence CATTATT which is present also at the 3'-terminus of the 18 S rRNA coding region. In this case it is known that the situation is CATTA3' . TT. With various methods we determined that the precise 5'-cleavage site is CATT . 5'ATT.

Nucleotide sequence of the 5'-terminal coding region for pre-rRNA and mature 17S rRNA in Tetrahymena thermophila rDNA

The 5'-terminus of 35S pre-rRNA and mature 17S rRNA of Tetrahymena thermophila was mapped on cloned rDNA fragments by S1 nuclease protection experiments. A single site for transcription initiation was observed when pre-rRNA prepared by three different methods was used as RNA probe. These mapping results were unambiguously confirmed by sequencing the 5'-terminal region of in vitro capped 35S pre-rRNA. DNA sequence analysis of about 520 nucleotides upstream of the transcription initiation site revealed several distinct sets of highly conserved repeat sequences. In addition, the 840 nucleotides downstream of the transcription initiation site (+ 1) was determined and shown to include the 5'-terminus of the 17S rRNA coding region at position + 647. A region surrounding the position + 195 contains an inverted repeat sequence which could be the structural basis for the recently described premature transcription termination event in this organism (Kister et al. (1983) Nucl. Acids Res. 11, 3487-3502).

The external transcribed spacer and preceding region of Xenopus borealis rDNA: comparison with the corresponding region of Xenopus laevis rDNA

We report sequence data from a cloned rDNA unit from Xenopus borealis, extending leftwards from the 18S gene to overlap a region previously sequenced by R. Bach, B. Allet and M. Crippa (Nucleic Acids Research 9, 5311-5330). Comparison with data from other species of Xenopus leads to the inference that the transcription initiation site in X.borealis is in the newly sequenced region and not, as was previously thought, in the region sequenced earlier. The X.borealis external transcribed spacer thus defined is some 612 nucleotides long, about 100 nucleotides shorter than in X.laevis. The X.borealis and X.laevis external transcribed spacers show a pattern of extensive but interrupted sequence divergence, with a large conserved tract starting about 100 nucleotides downstream from the transcription initiation site and shorter conserved tracts elsewhere. The regions in between the conserved tracts differ in length between the respective external transcribed spacers indicating that insertions and deletions have contributed to their divergence, as previously inferred for the internal transcribed spacers. Much of the overall length difference is in the region flanking the 18S gene, where there are also length microheterogeneities in X.laevis rDNA. As in X.laevis, the transcribed spacer sequences flanking the 18S gene in X.borealis contain no major tracts of mutual complementarity. The accumulated data on transcribed spacers in Xenopus render it unlikely that processing of ribosomal precursor RNA involves interaction between the regions flanking 18S RNA.

Location of the initial cleavage sites in mouse pre-rRNA

The locations of three cleavages that can occur in mouse 45S pre-rRNA were determined by Northern blot hybridization and S1 nuclease mapping techniques. These experiments indicate that an initial cleavage of 45S pre-rRNA can directly generate the mature 5' terminus of 18S rRNA. Initial cleavage of 45S pre-rRNA can also generate the mature 5' terminus of 5.8S rRNA, but in this case cleavage can occur at two different locations, one at the known 5' terminus of 5.8S rRNA and another 6 or 7 nucleotides upstream. This pattern of cleavage results in the formation of cytoplasmic 5.8S rRNA with heterogeneous 5' termini. Further, our results indicate that one pathway for the formation of the mature 5' terminus of 28S rRNA involves initial cleavages within spacer sequences followed by cleavages which generate the mature 5' terminus of 28S rRNA. Comparison of these different patterns of cleavage for mouse pre-rRNA with that for Escherichia coli pre-rRNA implies that there are fundamental differences in the two processing mechanisms. Further, several possible cleavage signals have been identified by comparing the cleavage sites with the primary and secondary structure of mouse rRNA (see W. E. Goldman, G. Goldberg, L. H. Bowman, D. Steinmetz, and D. Schlessinger, Mol. Cell. Biol. 3:1488-1500, 1983).

Primary sequence of the 5'-terminal region of mouse 18 S rRNA and adjacent spacer. Implications for rRNA processing

Among the stepwise cleavage reactions involved in the processing of rRNA precursors in mammalian cells, an early event corresponds to the removal of the so-called 'external transcribed regions' which are located upstream 18 S rRNA sequence within the primary transcript. We have determined the primary sequence of the domain of mouse pre-rRNA which encompasses this early processing site and analyzed its structural features with reference to the other eukaryotic homologs available. The potential involvement of secondary structure features of rRNA precursors in the recognition process for cleavage is discussed.

Location of the initial cleavage sites in mouse pre-rRNA

The locations of three cleavages that can occur in mouse 45S pre-rRNA were determined by Northern blot hybridization and S1 nuclease mapping techniques. These experiments indicate that an initial cleavage of 45S pre-rRNA can directly generate the mature 5' terminus of 18S rRNA. Initial cleavage of 45S pre-rRNA can also generate the mature 5' terminus of 5.8S rRNA, but in this case cleavage can occur at two different locations, one at the known 5' terminus of 5.8S rRNA and another 6 or 7 nucleotides upstream. This pattern of cleavage results in the formation of cytoplasmic 5.8S rRNA with heterogeneous 5' termini. Further, our results indicate that one pathway for the formation of the mature 5' terminus of 28S rRNA involves initial cleavages within spacer sequences followed by cleavages which generate the mature 5' terminus of 28S rRNA. Comparison of these different patterns of cleavage for mouse pre-rRNA with that for Escherichia coli pre-rRNA implies that there are fundamental differences in the two processing mechanisms. Further, several possible cleavage signals have been identified by comparing the cleavage sites with the primary and secondary structure of mouse rRNA (see W. E. Goldman, G. Goldberg, L. H. Bowman, D. Steinmetz, and D. Schlessinger, Mol. Cell. Biol. 3:1488-1500, 1983).

The complete nucleotide sequence of the rat 18S ribosomal RNA gene and comparison with the respective yeast and frog genes

The complete nucleotide sequence of the rat 18S ribosomal RNA gene has been determined. A comparison of the rat 18S ribosomal RNA gene sequence with the known sequences of yeast and frog revealed three conserved (stable) regions, two unstable regions, and three large inserts. (A,T) leads to (G,C) changes were more frequent than (G,C) leads to (A,T) changes for three comparisons (yeast leads to frog, frog leads to rat, and yeast leads to rat). GC pairs were inserted preferentially over AT pairs for the same three comparisons. These two factors contribute to the progressively higher GC content of 18S ribosomal RNA of yeast, frog, and rat.

Recognition signals for mouse pre-rRNA processing. A potential role for U3 nucleolar RNA

In order to identify signals for rRNA processing in eukaryotes, mouse pre-rRNA sequence features around four cleavage sites have been analyzed. No consensus sequence can be recognized when the four boundary regions are examined. Unlike mature rRNA termini, distal sequences of precursor-specific domains cannot participate in stable duplex with adjacent regions. The extensive divergence of precursor-specific sequences during evolution also applies to nucleotides adjacent to cleavage sites, with a significant exception for a conserved segment immediately downstream 5.8S rRNA. A specific role is proposed for U3 nucleolar RNA in the conversion of 32S pre-rRNA into mature 28S rRNA, through base-pairing with precursor-specific sequences at the boundaries of excised domains.

Multiple heterogeneities in the transcribed spacers of ribosomal DNA from Xenopus laevis

Ribosomal DNA (rDNA) from Xenopus laevis contains several heterogeneities in all three transcribed spacers, as revealed by analysis of cloned and uncloned amplified rDNA from oocytes and cloned chromosomal rDNA from erythrocytes. Heterogeneities include single base changes and length variants of one to several nucleotides. Sites of variation are widely but non-uniformly distributed, some occurring only a short distance outside the boundaries of the rRNA coding regions. No two transcription units that we have yet examined are identical throughout their transcribed spacer regions.

Nucleotide sequence of the 5'-terminal region of rat 18S ribosomal DNA

The 5'-terminal 597 base-pairs (bp) of the Sprague-Dawley rat 18S ribosomal RNA gee and 10 bp of the adjoining transcribed spacer have been sequenced. Previously sequenced 10 large oligonucleotides of rat 18S RNA were located in this region. This mammalian sequence has been compared with the known sequences of yeast and frog 18S rDNA's. The analysis indicates that 534 bp of the 597 bp (89%) are conserved between rat and frog sequences but only 75% of the nucleotides are conserved between rat and yeast in this region. Two large and two small sections have been identified where insertions have been introduced during evolution. Of these 58 bp long inserted sections of the rat rDNA sequence, 50 bp (86%) were G-C base-pairs.

Transcription of cloned Xenopus laevis ribosomal DNA microinjected into Xenopus oocytes, and the identification of an RNA polymerase I promoter

Transcription of a cloned Xenopus laevis ribosomal DNA (rDNA) fragment, microinjected into Xenopus oocytes, is initiated at the in vivo 40S pre-ribosomal RNA (pre-rRNA) site (+/- 2 bp) by RNA polymerase I. An X. laevis RNA polymerase I promoter has been mapped by studying the transcription of in vitro rDNA mutants in the oocyte system. The active promoter lies within the DNA segment beginning 145 bp upstream, and most probably ending 16 bp downstream, from the 40S pre-rRNA initiation site (-145 bp to +16 bp). Furthermore, active promoter elements lie more than 35 bp upstream from the initiation site (-35 bp). The X. laevis RNA polymerase I promoter therefore lies mainly upstream from the 40S pre-rRNA initiation site. Independent deletion of three adjacent rDNA segments lying between -61 and +16 bp reduces promoter activity by a factor of more than 16. The central of these "null" deletions removes an oligo(T)6 motif at -27 bp that is in an analogous position to the Goldberg-Hogness (TATA) box of RNA polymerase II promoters.