A novel class of small nucleolar RNAs (snoRNAs), encoded in introns of protein coding genes and originating from processing of their precursor molecules, has recently been described. The L1 ribosomal protein (r‐protein) gene of Xenopus laevis and its human homologue contain two snoRNAs, U16 and U18. It has been shown that these snoRNAs are excised from their intron precursors by endonucleolytic cleavage and that their processing is alternative to splicing. Two sequences, internal to the snoRNA coding region, have been identified as indispensable for processing the conserved boxes C and D. Competition experiments have shown that these sequences interact with diffusible factors which can bind both the pre‐mRNA and the mature U16 snoRNA. Fibrillarin, which is known to associate with complexes formed on C and D boxes of other snoRNAs, is found in association with mature U16 RNA, as well as with its precursor molecules. This fact suggests that the complex formed on the pre‐mRNA remains bound to U16 throughout all the processing steps. We also show that the complex formed on the C and D boxes is necessary to stabilize mature snoRNA.
Saccharomyces cerevisiae snR30 is an essential box H/ACA small nucleolar RNA (snoRNA) required for the processing of 18S rRNA. Here, we show that the previously characterized human, reptilian, amphibian, and fish U17 snoRNAs represent the vertebrate homologues of yeast snR30. We also demonstrate that U17/snR30 is present in the fission yeast Schizosaccharomyces pombe and the unicellular ciliated protozoan Tetrahymena thermophila. Evolutionary comparison revealed that the 3-terminal hairpins of U17/snR30 snoRNAs contain two highly conserved sequence motifs, the m1 (AUAUUCCUA) and m2 (AAACCAU) elements. Mutation analysis of yeast snR30 demonstrated that the m1 and m2 elements are essential for early cleavages of the 35S pre-rRNA and, consequently, for the production of mature 18S rRNA. The m1 and m2 motifs occupy the opposite strands of an internal loop structure, and they are located invariantly 7 nucleotides upstream from the ACA box of U17/snR30 snoRNAs. U17/snR30 is the first identified box H/ACA snoRNA that possesses an evolutionarily conserved role in the nucleolytic processing of eukaryotic pre-rRNA.In eukaryotes, biogenesis of cytoplasmic ribosomes is a complex process that takes place mainly in the nucleolus (12, 27). The RNA polymerase I synthesizes the 18S, 5.8S, and 25/28S rRNAs within a large precursor rRNA (pre-rRNA) that also contains long externally (5Ј ETS and 3Ј ETS) and internally (ITS-1 and ITS-2) transcribed spacers (Fig. 1A). To release mature-size 18S, 5.8S, and 25/28S rRNAs, the noncoding spacer regions are removed by an ordered series of endo-and exonucleolytic cleavages. During processing, the maturing rRNAs associate with 80 ribosomal proteins to form the 40S and 60S ribosomal subunits. Maturation of rRNAs and their assembly into functional ribosomes require about 150 transacting protein and about the same number of small nucleolar RNA (snoRNA) factors (12, 27, 52).The snoRNAs, with the sole exception of 7-2/MRP, fall into two distinct families which contain either the evolutionarily conserved C (UGAUGA) and D (CUGA) or H (ANANNA) and ACA box motifs, which are essential for the expression, nucleolar accumulation, and function of snoRNAs (13,24,47,49,54). The two classes of snoRNAs are associated with two distinct sets of proteins to form small nucleolar ribonucleoproteins (snoRNPs). The box C/D snoRNAs are associated with the Snu13p (15.5-kDa), Nop56p, Nop58p, and Nop1p/fibrillarin snoRNP proteins; the box H/ACA snoRNAs are complexed with Gar1p, Nhp2p, Nop10p, and Cbf5p/dyskerin. The box C/D snoRNPs are responsible for the site-specific synthesis of the numerous 2Ј-O-methylated nucleotides in rRNAs, while the box H/ACA snoRNPs synthesize ribosomal pseudouridines (13,24,25,47). The snoRNAs specify the substrate nucleotides through forming transient base pairing interactions with the appropriate rRNA sequences. The 2Ј-O-methyltransferase (Nop1p/fibrillarin) and pseudouridine synthase (Cbf5p/dyskerin) enzymes are found among the snoRNP proteins.A few box C/D and H/ACA snoRNPs, however, func...
We report that the third intron of the Li ribosomal protein gene of Xenopus laevis encodes a previously uncharacterized small nucleolar RNA that we called U16. This snRNA is not independently transcribed; instead it originates by processing of the pre-mRNA in which it is contained. Its sequence, localization and biosynthesis are phylogenetically conserved: in the corresponding intron of the human Li ribosomal protein gene a highly homologous region is found which can be released from the pre-mRNA by a mechanism similar to that described for the amphibian U16 RNA. The presence of a snoRNA inside an intron of the Li ribosomal protein gene and the phylogenetic conservation of this gene arrangement suggest an important regulatory/functional link between these two components.
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