By construction and screen of mouse nucleolar cDNA library, a novel mammalian small nucleolar RNAs (snoRNA) was identified. The novel snoRNA. 7O nt in length, displays structural features typical of C/D box snoRNA family The snoRNA possesses an 11-nt-long rRNA antisence element and is predicted to guide the 2'-O-methylation of mouse 2gs rRNA at G4043. a site unknown so far to be modified in vertebrates. The comparison of functional clement of snoRNA guides among eukaryotes reveals that the novel snoRNA is a mammalian counterpart of yeast snR38 despite highly divergent sequence between them, Mouse and human snR38 and other cognates in distanl vertebrates were positively detected with slight length variability. As expected, the rRNA ribosc-mcthylation site predicted by mouse snR3g was precisely mapped by specific-primer extension assay. Furthermore. our analyses show that mouse and human snR38 gene have multiple variants and are nested in the introns of different host genes with unknown function. Thus. snR38 is a phylogenefcafiy conserved methylafion guide but exhibits different genomie organization in eukaryotes.

Using a powerful computer-assisted analysis strategy, a large-scale search of small nucleolar RNA (snoRNA) genes in the recently released draft sequence of the rice genome was carried out. This analysis identi

The mitochondrial genome of the Chinese giant salamander Andrias davidianus was isolated using the long-and-accurate polymerase chain reaction (LA PCR) method. The sequencing work adopted the shotgun strategy accompanying with seven internal primers to cover the gaps where overlapping clones were not available. The entire mtDNA sequence is 16,503 bp long, with a gene content of 13 protein-coding, two ribosomal RNA and 22 transfer RNA genes, and order identical to that observed in most other vertebrates except for an additional 318 bp non-coding sequence between tRNA-Thr and tRNA-Pro genes. In order to carry out molecular phylogenetic analyses, all 13 protein sequences deduced from whole mitochondrial genomes for eight vertebrate species (six amphibians, two lobe-finned fishes) were combined to a single data set. This data set was refined by the program Gblocks using a stringent parameter setting and then subjected to MP, ML and NJ analyses. Thus phylogenetic relationships among living amphibians were discussed.

Small nucleolar RNAs (snoRNAs) represent an abundant group of non-coding RNAs in eukaryotes. They can be divided into guide and orphan snoRNAs according to the presence or absence of antisense sequence to rRNAs or snRNAs. Current snoRNAsearching programs, which are essentially based on sequence complementarity to rRNAs or snRNAs, exist only for the screening of guide snoRNAs. In this study, we have developed an advanced computational package, snoSeeker, which includes CDseeker and ACAseeker programs, for the highly efficient and specific screening of both guide and orphan snoRNA genes in mammalian genomes. By using these programs, we have systematically scanned four human-mammal whole-genome alignment (WGA) sequences and identified 54 novel candidates including 26 orphan candidates as well as 266 known snoRNA genes. Eighteen novel snoRNAs were further experimentally confirmed with four snoRNAs exhibiting a tissue-specific or restricted expression pattern. The results of this study provide the most comprehensive listing of two families of snoRNA genes in the human genome till date.