U21, a novel small nucleolar RNA with a 13 nt. complementarity to 28S rRNA, is encoded in an intron of ribosomal protein L5 gene in chicken and mammals

Abstract

Following a search of sequence data bases for intronic sequences exhibiting structural features typical of snoRNAs, we have positively identified by Northern assays and sequence analysis another intron-encoded snoRNA, termed U21. U21 RNA is a 93 nt. long, metabolically stable RNA, present at about 10(4) molecules per HeLa cell. It is encoded in intron 5 of the ribosomal protein L5 gene, both in chicken and in the two mammals studied so far, human and mouse. U21 RNA is devoid of a 5'-trimethyl-cap and is likely to result from processing of intronic RNA. The nucleolar localization of U21 has been established by fluorescence microscopy after in situ hybridization with digoxigenin-labeled oligonucleotide probes. Like most other snoRNAs U21 contains the box C and box D motifs and is precipitated by anti-fibrillarin antibodies. By the presence of a typical 5'-3' terminal stem, U21 appears more particularly related to U14, U15, U16 and U20 intron-encoded snoRNAs. Remarkably, U21 contains a long stretch (13 nt.) of complementarity to a highly conserved sequence in 28S rRNA. Sequence comparisons between chicken and mammals, together with Northern hybridizations with antisense oligonucleotides on cellular RNAs from more distant vertebrates, point to the preferential preservation of this segment of U21 sequence during evolution. Accordingly, this complementarity, which overlaps the complementarity of 28S rRNA to another snoRNA, U18, could reflect an important role of U21 snoRNA in the biogenesis of large ribosomal subunit.

A Novel Brain-specific Box C/D Small Nucleolar RNA Processed from Tandemly Repeated Introns of a Noncoding RNA Gene in Rats

“…Total cell RNA was isolated by the method of Chomczynski and Sacchi (42) adapted to our conditions (43). Poly(A) ϩ RNA purification was performed as recommended by manufacturer (Promega).…”

“…3D and data not shown). In contrast, known ubiquitous intronic C/D box snoRNAs, whether they are encoded in protein genes or in noncoding RNAs, are conserved over a much larger span of vertebrate phylogeny (9,37,39,43,46). The three previously reported brain-specific C/D box snoRNAs also seem substantially more ancient than RBII-36, since their origin must predate the primates/rodents split during mammalian evolution (17).…”

“…RBII-36 snoRNA Is Only Detected in Rats-Most box C/D snoRNAs have homologues in distant vertebrate species that can be detected by Northern cross-hybridizations using oligonucleotide probes directed to their conserved antisense element (9,43,46). Given that the 3Ј half of RBII-36 snoRNA sequence is preferentially conserved among the different tandemly repeated units (Fig.…”

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.…”

“…We have recently identified a novel snoRNA, U21, encoded in an intron of the gene of ribosomal protein L5 in distant vertebrates, chicken, human and mouse [14]. U21 is remarkable *Corresponding author.…”