A novel small nucleolar RNA (U16) is encoded inside a ribosomal protein intron and originates by processing of the pre-mRNA.

Abstract

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.

U17XS8, a small nucleolar RNA with a 12 nt complementarity to 18S rRNA and coded by a sequence repeated in the six introns ofXenopus laevisribosomal protein S8 gene

“…This peculiar mechanism has been demonstrated to be involved also in the production of the other snoRNAs recently found to be encoded in introns, U14, U15 U16 and HeLa U17 RNAs (7)(8)(9)41). In the case of U16 RNA, encoded in an intron of the Xenopus gene for r-protein L1, it has been shown that its production is alternative to that of the mature Li mRNA (8). As for U17XS8, we have shown that also the microinjection of a short intronic transcript bearing the U17Xs8 sequence leads to the production of the mature product.…”

“…We show here that the sequences repeated in the introns of S8a gene, on the contrary, code for a small nucleolar RNA (snoRNA), which we named Ul7Xs8 RNA, presumably involved in ribosome production. Similar genome organizations, with snoRNAs encoded in the introns of other genes, are being found with increasing frequency: U14 RNA (6), U15 RNA (7), U16 RNA (8), U17 RNA (9) and U20 RNA (Caizergues-Ferrer, personal communication). We have adopted the name 'U 17' for the Xenopus S8a intron encoded snoRNA after consideration of the strong homology with the U17 RNA described in HeLa cells (9), also called El RNA by Ruff et al (10); however, because of some relevant differences in structure and properties, we identify the Xenopus RNA with a specifying superscript.…”

“…In fact U14 RNA is encoded in three introns of the mouse gene for cognate hsc70 heat shock protein (6,41), U16 RNA in the third intron of the gene for Xenopus r-protein L1 (8), U15 RNA in the first intron of the gene for human r-protein S3 (7), and U20 RNA in one intron of the gene for vertebrate nucleolin (CaizerguesFerrer, personal communication). These examples are numerous enough to permit the conclusion that this gene organization is not coincidental but must have an important functional relevance.…”

Position within the host intron is critical for efficient processing of box C/D snoRNAs in mammalian cells

“…A common feature of mammalian snoRNA host gene transcripts is a 5Ј terminal oligopyrimidine sequence, whose precise function with respect to snoRNA synthesis is unknown (14,15). In most cases, it appears that snoRNAs are released from excised, debranched introns by exonucleolytic trimming (16)(17)(18); a minor pathway involves endonucleolytic cleavage of flanking intron sequences (19,20). Many yeast snoRNAs are transcribed as monocistronic or polycistronic precursors from independent transcription units, and proteins involved in their processing have been characterized (21)(22)(23).…”

SnoRNA U21 is also intron‐encoded in Drosophila melanogaster but in a different host‐gene as compared to warm‐blooded vertebrates

“…Particularly, a growing family of snoRNAs contain long, phylogenetically conserved sequence complementarities to rRNAs, which must reflect the biological importance of their transient pairing with pre-rRNA in the nucleolus [4]. Moreover, most of the newly identified snoRNAs exhibit a unique biosynthetic pathway [5][6][7][8][9][10][11][12][13][14][15][16][17][18]. Not only they are encoded in introns of protein-coding genes, but they result from a novel form of intronic RNA processing of their host-gene transcript.…”