Characterization of three novel snoRNAs from Schizosaccharomyces pombe implies the structural and functional diversity of box H/ACA snoRNA family

Site-specific pseudouridylations of rRNAs and snRNAs are directed by small guide RNAs that usually possess conserved II and ACA motifs and the consensus secondary structure consisting of hairpin-hinge-hairpin-tail. In this study, through screening cDNA library, three novel box II/ACA snoRNAs, termed SP12, SP16 and SP20, have been identified from fisson yeast Schizosacchromyces pombe. Each of the small RNAs possesses an ACA-like motif and exhibits secondary structures containing two or three large hairpin-like domains. Although the box II is noncanonical, SP20 can be potentially folded into a typical box II/ACA snoRNA-like structure and is predicted to guide two pseudouridylations, U1208 and U1053, on 18S rRNA. In contrast, SP12 and SP16 display different structures from SP20 and have no antisense elements to rRNAs or snRNAs. Obviously, they are new members of orphan guide snoRNAs whose functions remain elusive. The genes encoded for SP12 and SP16 are both located in long intergenic regions between protein-coding genes. A post-transcriptional processing for SP16 precursor was demonstrated. Interestingly, SP20 gene is nested inside a very hypothetical ORF, but transcribed in a reverse sense. Northern and RT-PCR analyses could not detect the transcript from the hypothetical ORF, and therefore exclude the expression of the spurious gene. This is the first example that a genetic locus predicted for protein-coding gene actually encodes a small non-messenger RNA in S. pombe.