User:Battlego/U3 snoRNA



The U3 snoRNA is an exceptional member of the box C/D subclass. It is much longer than typical box C/D snoRNAs and does not direct chemical modifications. Instead, it acts as an RNA-chaperone mediating structural changes of the pre-rRNA to establish the correct conformation endonuclease cleavage.

Together with two other snoRNAs, mammalian U8 and U13, it shares some features with snRNAs. For instance, human U3 snoRNA, has a hypermethylated 2,2,7-trimethylguanosine (TMG) cap at their 5' end. U3 snoRNAs are processed from primary transcripts with a rather particular promoter, which may represent the fusion of two promoter systems: Homo1 D-box and TATA-box.

In the first stage, a 3'-extended precursor with a mono-methylated cap, which is then trimmed at the 3' end. The length of U3 varies by more than a factor of three from 143nt in Trypanosoma to 442nt in Candida glabrata. Its sequence is highly variable appart from several short highly conserved boxes denoted by A', A, C', B, C, and D, where C and D define the membership in box C/D class of snoRNAs.

Phylogenetic Range of U3 snoRNA
The U3 snoRNA is highly structured and exhibits several conserved structural domains. Due to its pivotal function in rRNA maturation, the U3 snoRNAs is belived to be ubiquitously present in Eukaryotes. More than 230 eukaryotic genomes are known so far.

Introns of U3 snoRNA


Introns in U3 snoRNA genes have been described in the literature for S. cerevisae and H. wingei. Over all, the introns in the U3 snoRNA genes are evolutionarily very flexible. For example, there are Kluyveromyces species with and without introns.

All Saccharomyces sp. contain an intron located as described previously at 14th nucleotide of U3 snoRNA, directly upstream of box A. For other saccharomycotina no intron is known.

Within sordariomycetes three genera with introns that are phylogentically interspersed lineages are known without introns: Trichoderma reesei, Neurospora sp., and Magnaparthe grisae.

Introns are also present in all eurotiomycetidae except Ascosphaera apis. In Uncinocarpus reesii and Coccidioides sp., the intron was located within the loop of M1 and thus within box A. In contrast, Histoplasma capsulatum and Paracoccidioides brasiliensis have the intron at the typical position, i.e., after the 14th nucleotide, just upstream of the A box.

Promoters of U3 snoRNA
Metazoan U3 snoRNAs have snRNA-like promoters with a very well-conserved proximal sequence element (PSE). In several cases, there is also a canonical TATA-box, although most metazoans exhibit only a weak or no TATA-box. Closely related species may show differ in this respects: For instance, Anopheles gambiae and Bombyx mori have no TATA-box, which is present in Apis mellifera.