Identification and characterization of two novel box HACA snoRNAs from Schizosaccharomyces pombe

Through constructing a specialized cDNA library based on small RNAs isolated from partial purified nuclei of Schizosaccharomyces pombe, two novel noncoding RNAs, termed Sp15-70 and Sp18-61, have been identified. Bioinformatics analysis reveals that both the novel RNAs possess a typical secondary structure of box HACA snoRNA and antisense elements to rRNAs. According to the relationship between the structure and function of box HACA snoRNA, Sp15-70 was predicted to direct pseudouridylation in 25S rRNA at U2401 and U2298; Sp18-61 was predicted to direct pseudouridylation in 18S rRNA at U208 and 25S rRNA at U2341. The four predicted pseudouridylation sites were all verified experimentally by the CMC-primer extension analysis. Both Sp15-70 and Sp18-61 were encoded by single copies which were located in the intergenic regions between the CDS of two protein-coding genes on chromosome Ⅰ and Ⅲ of S. pombe, respectively. Putative TATA-like elements can be found upstream from the 5′ end of these snoRNA genes, suggesting that they could be transcribed from their own promoters. Comparison of the two snoRNAs and their functional homologues in diverse organisms reveals that extensive recombinations among different snoRNAs have occurred during the evolution from their primitive progenitors.