Identification Of U43 And Its Neighboring SnoRNAs And Analyses Of Their Genomic Organization And Expression

Small nucleolar RNA (snoRNA) is nucleolus-localised noncoding RNA which direct the site-specific formation of the two prevalent types of rRNA and snRNA modified mucieotides, 2'-O-methylated nucleotides and pseudouridines. Identify more snoRNAs and explore their genomic organizations are significant for studying the structure, founction and expression of snoRNA.In this paper, 29 novel U43 and 37 novel snoRNAs flanking U43 (including 27 box C/D snoRNA and 10 box H/ACA snoRNA) were identified by using mutiple computational strategies including snoSCAN, snoGPS and comparative sequence analysis. Novel U43 were conserved in C, D, C', D' boxes and antisense element corresponding to C1707 of human 18s rRNA. 10 novel box H/ACA snoRNA found in plant are homologues for each other defined by their antisense element. All 66 novel snoRNAs were named according to snoRNA nomenclature.Mfold were used to predict the secondary structure of novel box H/ACA snoRNA, and nine of ten showed the "hairpin-hinge-hairpin-tail"structure and ACA box located three nucleotides upstream of 3' end. Potential base-pairing interactions between the snoRNA and rRNA were predicted. The novel snoRNA in arabidopsis was predictied to direct the pseudouridylation on U1311 of 25s rRNA. No homologue of it has been identified before in plant. It was named snoR205.Together with novel U43s identified in this paper and U43s reported before, the sequences of 44 U43 have been analysised. In eukaryotes, U43s are single-functional, they guide the methylation of a universial methylated site; in archaea, sR12 is multiple-functional snoRNA directing methylation for several sites of rRNA.By using GENSCAN and Splice Site Prediction by Neural Network et al., the genomic organization and expression of U43 have been studied. Our results demonstrated U43 showed complexy genomic organization in differernt organisms. The newly identified snoRNA gene organization, a non-coding RNA gene encodes two different types of snoRNAs by its exon and intron, was identified as well as intron-encoded snoRNA, independent transcribed snoRNA and polycistronic snoRNA cluster.By using construction of cDNA clones and sequencing, we verified our prediction...