Structure of mouse rRNA precursors. Complete sequence and potential folding of the spacer regions between 18S and 28S rRNA

Nucleotide sequence of the 17S-25S spacer region from rice rDNA

The nucleotide sequence of a spacer region between rice 17S and 25S rRNA genes (rDNAs) has been determined. The coding regions for the mature 17S, 5.8S and 25S rRNAs were identified by sequencing terminal regions of these rRNAs. The first internal transcribed spacer (ITS1), between 17S and 5.8S rDNAs, is 194-195 bp long. The second internal transcribed spacer (ITS2), between 5.8S and 25S rDNAs, is 233 bp long. Both spacers are very rich in G+C, 72.7% for ITS1 and 77.3% for ITS2. The 5.8S rDNA is 163-164 bp long and similar in primary and secondary structures to other eukaryotic 5.8S rDNAs. The 5.8S rDNA is capable of interacting with the 5' terminal region of 25S rDNA.

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.

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.

Chemically modified nucleic acids as immunodetectable probes in hybridization experiments

Guanine residues in nucleic acids can be modified by treatment with N-acetoxy-N-2-acetylaminofluorene and its 7-iodo derivative in an in vitro nonenzymatic reaction. The modified nucleic acids (ribo or deoxyribo, single or double stranded) are recognized by specific antibodies. They can be immunoprecipitated or used as probes in hybridization experiments and detected by immunochemical techniques.

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.

The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes

We have determined the complete nucleotide sequence (4712 nucleotides) of the mouse 28S rRNA gene. Comparison with all other homologs indicates that the potential for major variations in size during the evolution has been restricted to a unique set of a few sites within a largely conserved secondary structure core. The D (divergent) domains, responsible for the large increase in size of the molecule from procaryotes to higher eukaryotes, represent half the mouse 28S rRNA length. They show a clear potential to form self-contained secondary structures. Their high GC content in vertebrates is correlated with the folding of very long stable stems. Their comparison with the two other vertebrates, xenopus and rat, reveals an history of repeated insertions and deletions. During the evolution of vertebrates, insertion or deletion of new sequence tracts preferentially takes place in the subareas of D domains where the more recently fixed insertions/deletions were located in the ancestor sequence. These D domains appear closely related to the transcribed spacers of rRNA precursor but a sizable fraction displays a much slower rate of sequence variation.

Complete nucleotide sequence of mouse 18 S rRNA gene: comparison with other available homologs

We present the complete sequence of mouse 18 S rRNA. As indicated by comparison with yeast, Xenopus and rat, the conservation of eukaryotic 18 S rRNA sequences is extensive. However, this conservation is far from being uniform along the molecule: most of the base changes and the size differences between species are concentrated at specific locations. Two distinct classes of divergent traces can be detected which differ markedly in their rates of nucleotide substitution during evolution, and should prove valuable in additional comparative analyses, both for eukaryotic taxonomy and for rRNA higher order organization. Mouse and rat 18 S rRNA sequences differ by only 14 point changes over the 1869 nucleotides of the molecule.

Nucleotide sequence of the 18S-26S rRNA intergene region of the sea urchin

The DNA sequence which spans the internal transcribed spacers of a cloned ribosomal transcription unit from the sea urchin, Lytechinus variegatus, has been determined. The region extends from the conserved Eco RI site near the 3' end of the 18S rDNA to a Bam HI site in the 26S rDNA and includes 232 nucleotides coding for 18S rRNA, 367 nucleotides of internal transcribed spacer, 159 nucleotides coding for 5.8S rRNA, 338 nucleotides of internal transcribed spacer, and 505 nucleotides coding for 26S rRNA. The rRNA coding regions were identified by direct analysis of 3'-labeled 18S and 5.8S rRNA and 5'-labeled 5.8S rRNA, and by sequence homology of the 26S rDNA with yeast and vertebrate 26/28S rRNAs. The internal transcribed spacers are GC-rich, similar to those of vertebrates. The 5.8S and 5' 26S rDNA sequences support a proposed model for a structural domain of the yeast large subunit ribosomal RNA (Veldman et al. [1981] Nucleic Acids Res. 9, 6935-6952).

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.

Improved methods for structure probing in large RNAs: a rapid 'heterologous' sequencing approach is coupled to the direct mapping of nuclease accessible sites. Application to the 5' terminal domain of eukaryotic 28S rRNA

We have developed a combined approach for probing native structures in large RNAs. In the first method, after digestion with a structure specific nuclease, accessible sites are mapped at sequence resolution along the entire RNA molecule which is used as a template for the reverse transcriptase elongation of a 5' end labelled selected primer (coding strand of a small restriction fragment of the cloned gene). This method circumvents any prior end-labelling of RNA, a technique with major limitations for large RNAs. In the second approach, a rapid "heterologous" sequencing can be easily applied to definite domains of an RNA molecule in a variety of species (or individuals), without additional DNA cloning nor end-labelling of RNA. By taking advantage of the presence of evolutionary conserved tracts within an RNA sequence, it allows a rapid analysis of RNA folding patterns in terms of phylogenetic comparisons : when located within such a conserved tract, selected restriction fragments from a cloned gene can be used as heterologous primers for sequencing the upstream divergent region in RNAs of other species by currently available technology, i.e. reverse transcriptase elongation in the presence of chain terminator dideoxynucleotides.

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.