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

snoRNPs: Functions in Ribosome Biogenesis

Ribosomes are perhaps the most critical macromolecular machine as they are tasked with carrying out protein synthesis in cells. They are incredibly complex structures composed of protein components and heavily chemically modified RNAs. The task of assembling mature ribosomes from their component parts consumes a massive amount of energy and requires greater than 200 assembly factors. Among the most critical of these are small nucleolar ribonucleoproteins (snoRNPs). These are small RNAs complexed with diverse sets of proteins. As suggested by their name, they localize to the nucleolus, the site of ribosome biogenesis. There, they facilitate multiple roles in ribosomes biogenesis, such as pseudouridylation and 2′-O-methylation of ribosomal (r)RNA, guiding pre-rRNA processing, and acting as molecular chaperones. Here, we reviewed their activity in promoting the assembly of ribosomes in eukaryotes with regards to chemical modification and pre-rRNA processing.

A RAC protein-binding site in the internal transcribed spacer 2 of Pre-rRNA transcripts from Schizosaccharomyces pombe

The interdependence of steps in the processing of the eukaryotic preribosomal rRNA transcripts indicate that rRNA processing, at least in part, acts as a quality control mechanism to help ensure that only functional rRNA is incorporated into mature ribosomes. In search of structural components that underlie this interdependence, we have isolated a large protein complex or RAC that contains an independent binding site for all four of the transcribed spacers in the nascent pre-rRNA. In this study the RAC-binding site in the internal transcribed spacer 2 sequence of Schizosaccharomyces pombe rRNA transcripts was identified, and the influence of this site on rRNA maturation was assessed. Modification exclusion analyses indicate that the protein complex interacts with a helical domain previously shown to contain features common to both the internal transcribed spacer 1 and the 3'-external transcribed spacer. Mutagenic analyses in vitro confirm an interaction with this sequence, and parallel analyses in vivo indicated a critical role in both the maturation of the rRNA components of the large subunit as well as the 18 S rRNA component of the small subunit. Hybridization analyses also indicated greatly elevated levels of unprocessed nascent RNA. These effects are contrasted with mutations in other regions of the secondary structure that resulted in some reduction of plasmid-derived mature rRNA but no elevated levels of the precursor molecules. The significance with respect to rRNA maturation and the interdependences in rRNA processing are discussed.

U3 snoRNA may recycle through different compartments of the nucleolus

A model is proposed in which U3 small nucleolar RNA (snoRNA) is recruited from an inactive, stored form in the dense fibrillar component (DFC) of the nucleolus to an active form that is associated with the initial ribosomal RNA (rRNA) precursor. The initial steps of rRNA processing occur in the DFC, and then it is proposed that the U3 snoRNA moves with intermediates in rRNA processing from the DFC to the granular component (GC) of the nucleolus. The nucleolar protein fibrillarin is located primarily in the DFC, and it is suggested that the complex of fibrillarin and U3 snoRNA dissociates when U3 snoRNA transits to the GC. Finally, when U3 snoRNA is released from the processed rRNA, the tether holding the rRNA in the nucleolus is broken and rRNA can then be exported from the nucleolus to the cytoplasm. U3 snoRNA is hypothesized to recycle back from the GC to the DFC where it is stored until future association with another initial rRNA precursor. Data supporting this model are summarized. U3 snoRNA is also stored in the coiled body of interphase cells and in the nucleolar remnants and prenucleolar bodies of mitotic cells, and there may be some similarity in the binding sites for stored U3 snoRNA in the DFC and in these structures.

Delocalization of some small nucleolar RNPs after actinomycin D treatment to deplete early pre-rRNAs

Retention of some components within the nucleolus correlates with the presence of rRNA precursors found early in the rRNA processing pathway. Specifically, after most 40S, 38S and 36S pre-rRNAs have been depleted by incubation of Xenopus kidney cells in 0.05 microg/ml actinomycin D for 4 h, only 69% U3 small nucleolar RNA (snoRNA), 68% U14 snoRNA and 72% fibrillarin are retained in the nucleolus as compared with control cells. These nucleolar components are important for processing steps in the pathway that gives rise to 18S rRNA. In contrast, U8 snoRNA, which is used for 5.8S and 28S rRNA production, is fully retained in the nucleolus after actinomycin D treatment. Therefore, U8 snoRNA is in a different category than U3 and U14 snoRNA and fibrillarin. It is proposed that U3 and U14 snoRNA and fibrillarin, but not U8 snoRNA, bind to the external transcribed spacer or internal transcribed spacer 1, and when these binding sites are lost after actinomycin D treatment some of these components cannot be retained in the nucleolus. Other binding sites may also exist, which would explain why only some and not all of these components are lost from the nucleolus.

Small nucleolar RNA

A growing list of small nucleolar RNAs (snoRNAs) has been characterized in eukaryotes. They are transcribed by RNA polymerase II or III; some snoRNAs are encoded in the introns of other genes. The nonintronic polymerase II transcribed snoRNAs receive a trimethylguanosine cap, probably in the nucleus, and move to the nucleolus. snoRNAs are complexed with proteins, sometimes including fibrillarin. Localization and maintenance in the nucleolus of some snoRNAs requires the presence of initial precursor rRNA (pre-rRNA). Many snoRNAs have conserved sequence boxes C and D and a 3' terminal stem; the role of these features are discussed. Functional assays done for a few snoRNAs indicate their roles in rRNA processing for cleavage of the external and internal transcribed spacers (ETS and ITS). U3 is the most abundant snoRNA and is needed for cleavage of ETS1 and ITS1; experimental results on U3 binding sites in pre-rRNA are reviewed. 18S rRNA production also needs U14, U22, and snR30 snoRNAs, whereas U8 snoRNA is needed for 5.8S and 28S rRNA production. Other snoRNAs that are complementary to 18S or 28S rRNA might act as chaperones to mediate RNA folding. Whether snoRNAs join together in a large rRNA processing complex (the "processome") is not yet clear. It has been hypothesized that such complexes could anchor the ends of loops in pre-rRNA containing 18S or 28S rRNA, thereby replacing base-paired stems found in pre-rRNA of prokaryotes.

Cell cycle redistribution of U3 snRNA and fibrillarin. Presence in the cytoplasmic nucleolus remnant and in the prenucleolar bodies at telophase

The distribution of the U3 small nuclear RNA during the cell cycle of the CHO cell line was studied by in situ hybridization using digoxigenin-labelled oligonucleotide probes. The location of the hybrids by immunofluorescence microscopy and at the ultrastructural level was correlated with the distribution of two nucleolar proteins, nucleolin and fibrillarin. The U3 snRNA molecules persist throughout mitosis in close association with the nucleolar remnant. U3 snRNA is present in the prenucleolar bodies (PNBs) and could participate in nucleologenesis in association with several nucleolar proteins such as nucleolin and fibrillarin. The interaction of U3 snRNP with the 5' external spacer of pre-RNA newly synthesized by active NORs is proposed to be the promoting event of nucleologenesis.

Nucleolar localization of myc transcripts

In situ hybridization has revealed a striking subnuclear distribution of c-myc RNA transcripts. A major fraction of the sense-strand nuclear c-myc transcripts was localized to the nucleoli. myc intron 1-containing RNAs were noticeably absent from nucleoli, accumulating instead in the nucleoplasm. The localization of myc RNA to nucleoli was shown to be common to a number of diverse cell types, including primary Sertoli cells and several cell lines. Furthermore, nucleolar localization was not restricted to c-myc and N-myc and myoD transcripts also displayed this phenomenon. In contrast, gamma-actin or lactate dehydrogenase transcripts did not display nucleolar localization. These observations suggest a new role for the nucleolus in transport and/or turnover of potential mRNAs.

Nucleolar localization of myc transcripts

In situ hybridization has revealed a striking subnuclear distribution of c-myc RNA transcripts. A major fraction of the sense-strand nuclear c-myc transcripts was localized to the nucleoli. myc intron 1-containing RNAs were noticeably absent from nucleoli, accumulating instead in the nucleoplasm. The localization of myc RNA to nucleoli was shown to be common to a number of diverse cell types, including primary Sertoli cells and several cell lines. Furthermore, nucleolar localization was not restricted to c-myc and N-myc and myoD transcripts also displayed this phenomenon. In contrast, gamma-actin or lactate dehydrogenase transcripts did not display nucleolar localization. These observations suggest a new role for the nucleolus in transport and/or turnover of potential mRNAs.

An experimental study of Saccharomyces cerevisiae U3 snRNA conformation in solution

The conformation of Saccharomyces cerevisiae U3 snRNA (snR17A RNA) in solution was studied using enzymatic and chemical probes. In vitro synthesized and authentic snR17A RNAs have a similar conformation in solution. The S. cerevisiae U3 snRNA is folded in two distinct domains. The 5'-domain has a low degree of compactness; it is constituted of two stem-loop structures separated by a single-stranded segment, which has recently been proposed to basepair with the 5'-ETS of pre-ribosomal RNA. We demonstrate that, as previously proposed, the 5'-terminal region of U3 snRNA has a different structure in higher and lower eukaryotes and that this may be related to pre-rRNA 5'-ETS evolution. The S. cerevisiae U3 snRNA 3'-domain has a cruciform secondary structure and a compact conformation resulting from an higher order structure involving the single-stranded segments at the center of the cross and the bottom parts of helices. Compared to tRNA, where long range interactions take place between terminal loops, this represents another kind of tertiary folding of RNA molecules that will deserve further investigation, especially since the implicated single-strands have highly evolutionarily conserved primary structures that are involved in snRNP protein binding.

Organization of the gene family encoding mouse U3B RNA: role of gene conversions in its concerted evolution

In mouse, U3B small nuclear RNA is encoded by a small family of four functional genes. Three of these genes have recently been identified, with two of them being located 5 kb apart, in the same orientation [Mazan and Bachellerie, J. Biol. Chem. 263 (1988) 19461-19467]. By analyzing a cosmid library of mouse genomic DNA we have isolated the fourth gene, U3B.4, which is located 12 kb downstream from the previously reported pair of linked genes, U3B.1 and U3B.2, in the same orientation. Its sequence analysis demonstrates that four mouse U3B genes have undergone a very efficient concerted evolution, with a perfect sequence identity not only over the entire RNA coding region but also over 254 bp of 5' flanking DNA which contain essential transcription signals. Moreover, in the regions which immediately flank the domain of perfect sequence identity, a patchwork of sequence similarities among the four genes is apparent, with a series of striking reversals in relationships between adjacent localized areas. This suggests that gene conversions have played a major role in the concerted evolution of the U3B gene family. A superimposition of conversion events, which probably occurred at distinct stages of rodent evolutions can be inferred. This has involved not only the three clustered copies, but also the remaining gene, U3B.3, the location of which relative to the cluster remains unknown. B1 repetitive elements are found at the boundaries of conversion domains, suggesting their possible role in control of the sequence homogenization process.

In vitro processing at the 3'-terminal region of pre-18S rRNA by a nucleolar endoribonuclease

In an investigation of the possible involvement of a highly purified nucleolar endoribonuclease in processing of pre-rRNA at the 3' end of the 18S rRNA sequence, an in vitro synthesized pre-18S rRNA transcript containing the 3' end region of 18S rRNA and the 5' region of the first internal transcribed spacer (ITS1) was used as a substrate for the enzyme. Cleavages generated by the nucleolar RNase were localized by S1 nuclease protection analysis and by the direct release of labeled rRNA products. Precise determination of the specificity of cleavage was achieved by RNA sequence analysis with end-labeled rRNA transcripts. These data demonstrated that the purified nucleolar RNase cleaved the pre-18S rRNA transcript at three specific sites relative to the 3' region of 18S rRNA. The first two sites included the mature 3'-end 18S rRNA sequence and a site approximately 55 nucleotides downstream of the 3'-end 18S rRNA sequence, both of which corresponded directly to recent results (Raziuddin, R. D. Little, T. Labella, and D. Schlessinger, Mol. Cell. Biol. 9:1667-1671, 1989) obtained with transfected mouse rDNA in hamster cells. The other cleavage occurred approximately 35 nucleotides upstream from the mature 3' end in the 18S rRNA sequence. The results from this study mimic the results obtained from in vivo studies for processing in the 3' region of pre-18S rRNA, supporting the proposed involvement of this nucleolar endoribonuclease in rRNA maturation.

In vitro processing at the 3'-terminal region of pre-18S rRNA by a nucleolar endoribonuclease

In an investigation of the possible involvement of a highly purified nucleolar endoribonuclease in processing of pre-rRNA at the 3' end of the 18S rRNA sequence, an in vitro synthesized pre-18S rRNA transcript containing the 3' end region of 18S rRNA and the 5' region of the first internal transcribed spacer (ITS1) was used as a substrate for the enzyme. Cleavages generated by the nucleolar RNase were localized by S1 nuclease protection analysis and by the direct release of labeled rRNA products. Precise determination of the specificity of cleavage was achieved by RNA sequence analysis with end-labeled rRNA transcripts. These data demonstrated that the purified nucleolar RNase cleaved the pre-18S rRNA transcript at three specific sites relative to the 3' region of 18S rRNA. The first two sites included the mature 3'-end 18S rRNA sequence and a site approximately 55 nucleotides downstream of the 3'-end 18S rRNA sequence, both of which corresponded directly to recent results (Raziuddin, R. D. Little, T. Labella, and D. Schlessinger, Mol. Cell. Biol. 9:1667-1671, 1989) obtained with transfected mouse rDNA in hamster cells. The other cleavage occurred approximately 35 nucleotides upstream from the mature 3' end in the 18S rRNA sequence. The results from this study mimic the results obtained from in vivo studies for processing in the 3' region of pre-18S rRNA, supporting the proposed involvement of this nucleolar endoribonuclease in rRNA maturation.

The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing

The first cleavage in mammalian pre-rRNA maturation occurs near the 5' end within the 5' external transcribed spacer. Using mouse cell extracts, we show that this processing is abolished by micrococcal nuclease pretreatment. Autoantibodies that recognize the U3, U8, and U13 snRNPs (anti-fibrillarin) deplete processing activity from the extract and selectively immunoprecipitate both rRNA substrates and processing products from the reaction. Specific involvement of the U3 snRNP is demonstrated by native gel electrophoresis of the processing reaction followed by Northern blotting and by oligonucleotide-directed RNAase H abolition of processing activity. Our identification of U3 function is discussed with respect to the molecular basis of pre-rRNA recognition by the U3 snRNP, possible roles of U3 and other nucleolar snRNPs in rRNA processing, and the morphological organization of the nucleolus and the ribosomal transcription complex.

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.

Molecular cloning of Xenopus fibrillarin, a conserved U3 small nuclear ribonucleoprotein recognized by antisera from humans with autoimmune disease

Autoantibodies against U3 small nuclear ribonucleoprotein are associated with scleroderma autoimmune disease. They were shown to react with fibrillarin, a 34- to 36-kilodalton protein that has been detected in all eukaryotes tested from humans to yeasts. We isolated a 1.6-kilobase cDNA encoding fibrillarin from a Xenopus laevis cDNA library. The protein contains a 79-residue-long Gly-Arg-rich domain in its N-terminal region and a putative RNA-binding domain with ribonucleoprotein consensus sequence in its central portion. This is the first report of cloning of fibrillarin, and the deduced protein sequence is in agreement with the involvement of the protein in a ribonucleoprotein particle.

Molecular cloning of Xenopus fibrillarin, a conserved U3 small nuclear ribonucleoprotein recognized by antisera from humans with autoimmune disease

Autoantibodies against U3 small nuclear ribonucleoprotein are associated with scleroderma autoimmune disease. They were shown to react with fibrillarin, a 34- to 36-kilodalton protein that has been detected in all eukaryotes tested from humans to yeasts. We isolated a 1.6-kilobase cDNA encoding fibrillarin from a Xenopus laevis cDNA library. The protein contains a 79-residue-long Gly-Arg-rich domain in its N-terminal region and a putative RNA-binding domain with ribonucleoprotein consensus sequence in its central portion. This is the first report of cloning of fibrillarin, and the deduced protein sequence is in agreement with the involvement of the protein in a ribonucleoprotein particle.

U3 small nuclear RNA (snR17A RNA) and DFR1 genes are very closely linked in Saccharomyces cerevisiae

SNR17A and DFR1 genes of Saccharomyces cerevisiae are only 313 bp apart and in the same orientation.

The 5' end of U3 snRNA can be crosslinked in vivo to the external transcribed spacer of rat ribosomal RNA precursors

From previous work it was known that U3 RNA is hydrogen bonded to nucleolar 28 S to 35 S RNA and can be covalently crosslinked to RNA of greater than 28 S by irradiation in vivo with long-wave ultraviolet light in the presence of 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT psoralen). Here we use a novel sandwich blot technique to identify these large nucleolar RNA species as rRNA precursors and to map the site(s) of crosslinking in vivo. The crosslink occurs between one or more residues near the 5' end of U3 RNA and a 380 nucleotide region of the rat rRNA external transcribed spacer (ETS1). We have sequenced this region of the rat ETS and we show that it includes an RNA-processing site analogous to those previously mapped to approximately 3.5 kb upstream from the 5' end of mouse and human 18 S rRNAs.

U3 small nuclear RNA can be psoralen-cross-linked in vivo to the 5' external transcribed spacer of pre-ribosomal-RNA

U3 small nuclear RNA is hydrogen-bonded to high molecular weight nucleolar RNA and can be isolated from greater than 60S pre-ribosomal ribonucleoprotein particles, suggesting that it is involved in processing of ribosomal RNA precursors (pre-rRNA) or in ribosome biogenesis. Here we have used in vivo psoralen cross-linking to identify the region of pre-rRNA interacting with U3 RNA. Quantitative hybridization selection/depletion experiments with clones of rRNA-encoding DNA (rDNA) and cross-linked nuclear RNA showed that all of the cross-linked U3 RNA was associated with a region that includes the external transcribed spacer (ETS) at the 5' end of the human rRNA precursor. To further identify the site of interaction within the approximately 3.7-kilobase ETS, Southern blots of rDNA clones were sandwich-hybridized with cross-linked RNA and then probed for cross-linked U3 RNA. These experiments showed that U3 RNA was cross-linked to a 258-base sequence between nucleotides +438 and +695, just downstream of the ETS early cleavage site (+414). The localization of U3 to this region of the rRNA precursor was not expected from previous models for a base-paired U3-rRNA interaction and suggests that U3 plays a role in the initial pre-rRNA processing event.

3'-end formation of mouse pre-rRNA involves both transcription termination and a specific processing reaction

We have studied the sequence requirements for 3'-end formation of rDNA transcripts in a cell-free system and show that the generation of correct ends of mouse pre-rRNA is brought about by a two-step process that involves a bona fide termination reaction, followed by a specific trimming of the primary transcript by 10 nucleotides. We show that termination of mouse ribosomal gene transcription by RNA polymerase I (pol I) takes place in front of an 18-bp DNA sequence element (the 'Sal box'), which was previously shown to function as termination signal. Termination of pol I transcription occurs at a fixed distance (11 bp) upstream of the Sal box, independent of the sequence of adjacent gene regions. The processing reaction, however, is strongly influenced by sequences flanking the termination signal at the 5' site. Substitution of a cluster of T residues by guanines within the region of 3'-end formation abolishes the 3'-terminal trimming of the primary transcript. Interestingly, this 3'-terminal processing event, which can be uncoupled from the termination reaction, requires both a correct 3' end and specific sequences in the 3'-terminal region of the primary transcript. Read-through transcripts generated in the extract system or by SP6 RNA polymerase are no substrate for the processing nuclease(s). Because the termination and processing activity can be separated chromatographically, the nucleolytic activity does not reside in TTF-I, the factor that binds to the Sal box and directs transcription termination.

An in vitro interaction between the human U3 snRNP and 28S rRNA sequences near the alpha-sarcin site

Model transcripts containing mammalian pre-rRNA sequences were incubated with a HeLa cell extract, digested with T1 RNase, and immunoprecipitated with anti-(U3)RNP or control antibodies. Two overlapping fragments derived from the 3' domain of human 28S rRNA were specifically immunoprecipitated although transcripts which spanned the transcription initiation site, the ETS processing site, the 5' end of 18S, and both termini of 5.8S yielded no protected fragments. The sequence of these fragments was determined using a novel technique in which the [32P]-labeled fragment was co-finger-printed with [3H]-labeled total transcript serving as an internal marker. The fragments immunoprecipitated derive from nucleotides 4570-4590 and 4575-4590 of human 28S and are adjacent to the alpha-sarcin site. Protection most likely involves the U3 RNA since it is sensitive to pretreatment of the extract with micrococcal nuclease. Complementarity between U3 and this rRNA region is phylogenetically conserved in species ranging from human to S. cerevisiae. The possible significance of this finding is discussed.

The sequence of U3 from Schizosaccharomyces pombe suggests structural divergence of this snRNA between metazoans and unicellular eukaryotes

We have cloned and sequenced one of the two genes encoding a 255 nucleotide small nuclear RNA from the fission yeast Schizosaccharomyces pombe. Based on the presence of four regions of primary sequence conservation and a predicted secondary structure similar to that previously proposed for human U3, we conclude that this molecule is the fission yeast homologue of this mammalian snRNA. The 5' one-third of fission yeast U3 is, however, unable to form a single stable hairpin as proposed for this region of the human RNA, but rather folds into two stem-loop structures. By analogy to fission yeast U3, we propose revised secondary structures containing two hairpins for this portion of the U3-like snRNAs from Saccharomyces cerevisiae and Dictyostelium discoideum. Thus, our data suggest that the structure of U3 snRNA has diverged in lower and higher eukaryotes.

SnR30: a new, essential small nuclear RNA from Saccharomyces cerevisiae

The gene for a previously unidentified small nuclear RNA has been cloned from Saccharomyces cerevisiae and its nucleotide sequence has been determined. The RNA, snR30, was mapped to a unique coding sequence 605 nucleotides long. SnR30 appears to be one of the most abundant snRNAs of S, cerevisiae in that it can be resolved by ethidium bromide staining on one-dimensional denaturing gels of total yeast RNA. Like other snRNAs, snR30 is enriched in nuclei preparations and possesses a trimethyl guanosine cap structure at its 5' end. After substituting one allele of the wild type gene in a diploid strain for a deleted gene, after sporulation, haploid strains carrying the deletion were unable to grow, indicating that snR30 is required for an essential, but as yet, unknown function. The nucleotide sequence close to the initiation site of the SNR30 gene is similar to that of other yeast SNR genes whose transcripts are associated with pre-rRNA, suggesting that snR30 is related to this group of snRNAs.

Sequence and genetic analysis of a dispensible 189 nucleotide snRNA from Saccharomyces cerevisiae

The structure of a Saccharomyces cerevisiae gene that encodes a small nuclear RNA (snRNA) of 189 nucleotides is described. This gene, designated SNR189, is located 400 base pairs upstream of the CRY1 gene on yeast chromosome III. Gene replacement analysis revealed the SNR189 gene to be dispensable for growth under a variety of culture conditions. The snR189 sequence lacks homology with other sequenced yeast or metazoan snRNAs.

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.

32S pre-rRNA processing: a dynamic model for interaction with U3RNA and structural rearrangements of spacer regions

A model of rearrangement of 32S pre-rRNA during processing was proposed. The first step of these events is the cotranscriptional interaction of the 3'-half of 5.8S rRNA and adjacent part of the internal transcribed spacer (ITS-2) with the 3'-part of the small nucleolar U3RNA from its 155th to 215th nucleotides (numbered for a rat U3RNA). This interaction prevents formation of intramolecular double-stranded structure between 5'-and 3'-end sequences of 5.8S rRNA. The second step is the appearance of extended hairpin structures in the ITS-2, which leads to a compactisation of the entire 32S-pre-rRNA molecule and to the complex formation between 5.8S rRNA and 28S rRNA sequences as the result of U3RNA displacing. After elimination of ITS-2 sequences from 32S pre-rRNA this complex can be included into ribosomes.

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.

Human U3 small nucleolar RNA genes are localized to the nucleoplasm

U3 RNA, an abundant, conserved, capped, small RNA localized to the nucleolar compartment of eukaryotic cells, its implicated in the processing of pre-ribosomal RNA. The genes for U1 and U2 snRNAs (small nuclear RNAs) are clustered and present in the nucleoplasmic DNA; however, the localization of U3 snRNA genes is not known. DNAs, isolated from HeLa cell nuclei and nucleoli, were hybridized with labeled probes corresponding to the 5'-flanking and the coding regions of the human U3 snRNA gene. The intensity of signals obtained with both the probes were 5-6 fold greater in nuclear DNA, compared to nucleolar DNA. With ribosomal gene probe, the nucleolar DNA had sixfold more intense signal than nuclear DNA. These results indicate that genes for U3 snRNA are in the nucleoplasm. Therefore, U3 snRNA, like 5S ribosomal RNA, appears to be synthesized in the nucleoplasm and transported to the nucleolus.

Plant small nuclear RNAs. II. U6 RNA and a 4.5SI-like RNA are present in plant nuclei

Two small nuclear RNA species (U6 RNA and a 4.5SI-like RNA) not described so far for plants were detected in broad bean (Vicia faba L.) nuclei. U6 RNA is 98 nucleotides long, contains psi and methylated nucleotides and shows a surprisingly high degree of sequence homology (80%) with its rat counterpart, particularly in the middle part (a 57 nucleotide-long stretch) of the molecule, where it amounts to 98%. The 4.5SI-like RNA, similar in its structure to 4.5SI RNA detected so far only in rodent nuclei, is 94 nucleotides long, contains psi and an unidentified nucleotide and exhibits 52% overall sequence homology with rat 4.5SI RNA. A block of 20 consecutive nucleotides at the 5' end of the molecule is conserved between broad bean 4.5SI-like RNA and rat 4.5SI RNA. The presence of the two RNA polymerase III internal promoter consensus sequences in 4.5SI-like RNA suggests that it is an RNA polymerase III transcript.

Small RNAs of Tetrahymena thermophila

Highly purified nuclear and cytoplasmic RNAs were obtained from Tetrahymena thermophila BVII containing only a minimal amount of cross-contamination. In the nuclear RNA fraction we have detected at least 6 distinct snRNAs. Some of the RNA species showed microheterogeneity. SnRNAs of Tetrahymena thermophila are very similar to rat snRNAs, as far as length is concerned. Our cytoplasmic small RNA fraction contained two RNAs, 7S and T7, reported recently as nuclear, particularly nucleolar RNAs. Moreover, we could detect only one cytoplasmic small RNA species Tc1, Tc2 was not observed. Neither the nuclear nor the cytoplasmic small RNA species are degradation products of ribosomal RNA as was shown by Northern blotting and following hybridization with pGY17 containing the entire transcribed region of the ribosomal DNA of Tetrahymena thermophila.

A U3 RNA pseudogene in mouse: sequence and organization in genomic DNA

A mouse U3 RNA pseudogene has been identified; it corresponds to a U3B full length coding sequence with a 3'-oligo(A) tail, precisely flanked at both ends by a pair of 15 bp direct repeats. These structural features suggest that it has arisen through an RNA-mediated mechanism involving an insertion at staggered nicks in the genome. Sequence data indicate that this mouse specimen has been generated by a different event as compared to the recently described rat pseudogenes. It represents the first reported case, for a pseudogene of this class, to be present at more than one copy per genome.

Multiple sequences in the Drosophila melanogaster U3 RNA gene are homologous to vertebrate U3 RNA

We have cloned and sequenced a DNA fragment from the genome of Drosophila melanogaster which is homologous to Novikoff hepatoma (rat) small nucleolar U3 RNA. DNA sequence analysis shows that the regions of homology between the cloned DNA and rat U3 RNA are distributed over the entire length of the molecule and the total homology of linear sequence is 53%. The present finding supports the generalization that U3 RNA has been evolutionally conserved but diverges between mammals and invertebrates. This clone contains the upstream and downstream sequences required for the efficient and correct transcription of small nuclear RNAs. The secondary structure proposed for the U3 RNA sequence deduced from the cloned DNA is similar in general topography to that reported for rat U3 RNA (Bernstein et al., ref. 23).

Isolation and characterization of a human U3 small nucleolar RNA gene

U3 RNA is an abundant, capped, small nucleolar RNA, implicated in the processing of preribosomal RNA. In this study, a DNA clone coding for U3 RNA (clone U3-1) was isolated from a human genomic library and characterized. The DNA sequence was identical to that of human U3 RNA isolated from HeLa cells. The flanking regions showed homology to the enhancer, promoter, and 3'-processing signal found in U1 and U2 snRNA genes. Further, the recently identified "U3 box" (GATTGGCTGCN10TATGTTAATTATGG) of rat U3 genes (Stroke and Weiner, (1985) J. Mol. Biol. 184, 183-193), was also found in the human U3 gene. This gene was transcribed in Xenopus oocytes; it is the first cloned true human U3 gene.

The evolution of eukaryotic ribosomal DNA

Mutations occur randomly throughout the ribosomal DNA (rDNA) sequence. Molecular drive (unequal crossing-over, gene conversion, and transposition) spreads these variations through the multiple copies of rDNA. Forces of selection act upon the variants to favor and fix them or disfavor and eliminate them. Selection has not permitted changes in regions within rRNA vital for its function; these sequences are evolutionarily conserved between diverse species. Possible functions for some of these conserved sequences are discussed. The secondary structure of rRNA is also highly conserved during evolution. However, eukaryotic rRNA is larger than prokaryotic rRNA due to blocks of "expansion segments". Arguments are put forward that expansion segments might not play any functional role. Other examples are reviewed of rDNA sequence insertion or deletion, including introns and the internal transcribed spacer 2.

Plant small nuclear RNAs. Nucleolar U3 snRNA is present in plants: partial characterization

Nuclei, isolated from a number of plant species by either of two independent, newly developed methods, regularly contained a common set of low-molecular-mass RNAs. Partial characterization of these RNAs, based on cell fractionation, polyacrylamide gel electrophoretic and chemical sequencing techniques, as well as comparison with literature data, revealed that, in addition to tRNA, 5S RNA and 5.8S RNA, plant nuclei contain two families of low-molecular-mass RNAs, that are counterparts of vertebrate U1 and U5 RNAs respectively, and three individual low-molecular-mass RNA species. One of these may be related to vertebrate U6 RNA. The two others are true eukaryotic U2 and U3 RNAs, respectively, on the basis of the following lines of evidence obtained from analyses of broad bean nuclear RNAs. The 3'-end portion (121 nucleotides sequenced) of broad bean U2 RNA shows a nearly perfect sequence homology with that of authentic pea U2 RNA. Broad bean U3 RNA is localized in the nucleolus and its 3'-end portion (164 nucleotides sequenced) (a) shows sequence homology with that of both rat U3 RNA (48%) and Dictyostelium D2 RNA (39%), (b) has a secondary structure which fits perfectly that proposed for both rat U3 RNA and Dictyostelium D2 RNA, and (c) contains the specific sequence which, in a model based on the primary structure of rat U3 RNA, is supposed to be involved in the processing of eukaryotic 32S pre-ribosomal RNA. This is the first report on the occurrence in plants of nucleolar U3 RNA.

Genes and pseudogenes for rat U3A and U3B small nuclear RNA

We report here the isolation and primary structure of two genes encoding rat U3 small nuclear RNA. One of the genes encodes U3B RNA; the other encodes an RNA which is almost identical to U3A RNA. Both genes are expressed after microinjection into the nuclei of Xenopus laevis oocytes and can direct the accumulation of mature U3 RNA as well as longer transcripts which may be the U3 precursors. We have also isolated and sequenced four other regions of the rat genome homologous to U3 RNA. One of these almost certainly represents a second U3B gene; the other three are pseudogenes which appear to have been generated by the reverse flow of genetic information from U3 RNA back into the genome. Using genomic blotting techniques, we show that the rat U3 genes are present in only a few copies per haploid genome and are probably not closely linked to one another.

Small nuclear RNAs in the ciliate Tetrahymena

We have isolated and partially characterized a family of small nuclear RNAs (snRNAs) from three different species of the protozoan Tetrahymena. We find six distinct snRNAs ranging in size from 100 to 250 nucleotides. The two largest snRNAs, as well as an abundant, heterogenous group of smaller snRNAs are found in the nucleolar RNA fraction. None of the snRNAs are transcription products of the ribosomal RNA gene or its flanking regions, as shown by hybridization tests. The snRNAs are metabolically stable as determined by pulse/chase experiments and several of them contain a number of modified nuclotides. The snRNAs from Tetrahymena all have slightly different sizes from mammalian snRNAs. The cap structure of the snRNAs from Tetrahymena differs from that of the snRNAs from mammalian cells, but has not yet been fully characterized. The relative amount of snRNAs to total RNA is less in Tetrahymena (greater than 0.1%) than in mammalian cells (2%).

Serum-induced stimulation of snRNA synthesis in mouse 3T3 fibroblasts

Small nuclear RNAs (snRNAs) from quiescent and serum-stimulated 3T3 cultures, labeled with [3H]uridine [( 3H]U), were electrophoresed in polyacrylamide-urea slab gels and revealed by staining with ethidium bromide and by fluorography. Judged by labeling with [3H]U, synthesis of 7S and U1-U6 RNAs was very low or absent in quiescent cultures. The serum-induced transition of 3T3 cells from a resting to a growing state was accompanied by an early, apparently sequential stimulation of snRNA synthesis; stimulated synthesis of 7S, U1, U2, U3, U4 and U6 RNAs coincided in time with serum-induced stimulation of 45S pre-ribosomal RNA (pre-rRNA) and heterogeneous nuclear RNA (hnRNA) synthesis.

Multiple states of U3 RNA in Novikoff hepatoma nucleoli

U3 RNA, a capped small nuclear RNA found thus far only in the nucleolus, has been implicated in the processing and/or transport of preribosomal RNA [Busch, H., Reddy, R., Rothblum, L., & Choi, Y. C. (1982) Annu. Rev. Biochem. 51, 617-654]. Tris(hydroxymethyl)aminomethane (Tris) (10 mM, pH 7.0) extracts of Novikoff hepatoma nucleoli, which contained about 80% of total nucleolar U3 RNA, were analyzed by sucrose density gradient centrifugation. Approximately 65% of the U3 RNA was bound to greater than 60S preribosomal ribonucleoprotein (RNP) particles, and about 15% sedimented at less than 20 S. The association between the 65% of U3 RNA that was bound to the preribosomal RNP particles was stable up to 55 degrees C. About 10% of U3 RNA was base paired to preribosomal RNA after deproteinization at 22 degrees C. The base-paired fraction of U3 RNA was released from the preribosomal RNA by heating to 45 degrees C or treating with 4 M urea. These results show that of the total nucleolar U3 RNP, (a) about 55% is bound to preribosomal RNP particles primarily by protein interactions, (b) about 10% is base paired to preribosomal RNA, (c) approximately 15% sedimented slowly and consisted presumably of free U3 RNP particles, and (d) the remaining 20% of U3 RNP was not extractable using 10 mM Tris buffer. On the basis of the different association states of U3 RNP particles, a model is proposed for the binding and dissociation events which take place between U3 RNP and preribosomal RNP particles.

Nature and origin of the RNA associated with simian virus 40 large tumor antigen

Simian virus 40 (SV40) large tumor (T) antigen isolated from mammalian cells undergoing lytic or transforming infection is associated with small RNA fragments ("T-antigen RNA") that are protected from nuclease digestion. The rather high complexity of the ribonuclease T1 fingerprints of T-antigen RNA suggested that it is mainly derived from cellular heterogeneous nuclear RNAs. In the present study, 5'-32P-labeled T-antigen RNA was hybridized to monkey, mouse, and human Alu and SV40 DNA, and the nucleotide sequence of 37 T1 oligonucleotides was determined. The results suggest that the bulk of T-antigen RNA is derived from noncoding, double-stranded, ordered regions of cellular heterogeneous nuclear RNAs that exhibit sequence homologies with interspersed repetitive elements of the cellular genome. The possible biological implications of these results are discussed.

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.