SUMMARY PARAGRAPH for SNR128
The small nucleolar RNAs (snoRNAs) are stable RNAs that are found within small nucleolar ribonucleoprotein complexes (snoRNPs) and localized to the nucleoli of eukaryotic cells. The majority of the snoRNAs are involved in ribosomal RNA processing, though some are also involved in processing of other RNAs and a couple have not yet been characterized as to their role in cells. Based on conserved sequence elements and association with conserved nucleolar proteins, the snoRNAs can be divided into three classes: box C/D snoRNAs, box H/ACA snoRNAs, and snoRNA MRP. Both the box C/D and box H/ACA families have many members, while MRP (produced by the NME1 gene) is the sole RNA of its type (6, 7). The box C/D and box H/ACA snoRNPs are found in all eukaryotes and even in Archaea, indicating that these are ancient and highly conserved complexes (8) For a complete listing of all the snoRNA genes in S cerevisiae, see the table of snoRNAs.
Box C/D snoRNAs
The box C/D snoRNAs are characterized by two short conserved sequence elements, called boxes C and D, near the 5' or 3'-end of the snoRNA respectively. The middle part may contain additional imperfect copies of the C and D boxes, referred to as C' and D' boxes. In addition, the C/D snoRNAs contain one or more sequences, from 10-22 nucleotides long, of perfect complementarity to the sequence of their target RNA molecule, most often either the 18S or 25S rRNAs (7, 8). Each box C/D snoRNA is bound by four evolutionarily conserved proteins to form a box C/D type small nucleolar ribonucleoprotein complex, or snoRNP (9): Nop1p (the homolog of vertebrate fibrillarin, 10), Nop58p, Nop56p, and Snu13p.
Most of the box C/D snoRNPs methylate the ribose moieties of nucleotides within the 18S or 25S rRNAs, a modification which, along with pseudouridylation, occurs immediately after transcription and prior to various cleavages to generate the mature 18S, 25S, and 5.8S rRNAs (6, 11, 4). See the tables of Modified Nucleotides in RNAs to view known methylation sites. The site of methylation is directed by base pairing between the snoRNA and the target RNA and occurs within the hybrid at a specific distance from the box D or D', but is catalyzed by the Nop1p methyltransferase (9). The function of methylating the ribosomal RNAs is not quite clear and loss of any particular methylation site, or the specific snoRNA that directs it, is generally tolerated with no phenotype (3). However, a total lack of 2'-O-ribose methylation may be lethal as a temperative sensitive allele of the Nop1p catalytic subunit that prevents methylation without preventing the cleavage steps is lethal (11). It is notable that the sites of modification are in functionally important regions and many are conserved across species (6, 12). In mammals, snRNAs involved in mRNA splicing are also methylated and mRNAs may also be methylated by box C/D snoRNPs with regulatory consequences (12).
The role of snoRNAs in converting the primary rRNA transcript into mature rRNAs
While most of the snoRNAs are not essential and are involved in RNA modification, either 2'-O-ribose methylation or pseudouridylation, a few, including members of each of the three families, are required for endonucleolytic cleavage steps in the processing to convert the primary rRNA transcript into the mature 18S, 5.8S, and 25S rRNA molecules (6, 4). Two box C/D snoRNAs, U3 (produced by two genes SNR17A and SNR17B) and U14 (produced by SNR128) and two box H/ACA snoRNPs, snR30 and snR10 are required for cleavage of the primary rRNA transcript. Depletion of U3, U14, or snR30 results in depletion of the 18S rRNA and complete lack of any one of these snoRNAs is lethal (6, 4). The snR10 snoRNA is not essential and its deletion produces only a mild reduction in 18S rRNA accumulation (4). U14 and snR10 are involved in both endonucleolytic cleavage steps and in targeting RNA modification reactions (4). In addition, RNase MRP is involved in endonucleolytic cleavage to produce the mature 5.8S rRNA molecule; its depletion produces lessened accumulation of the 5.8S rRNA. However, while RNase MRP is essential, it is not essential for rRNA processing as there is an alternative minor processing pathway (4).
The genomic organization of snoRNAs
The genomic organization of the box C/D snoRNAs in S. cerevisiae is notable in that it is quite variable. Some of these genes are encoded within the introns of protein coding genes, as is the case for vertebrate snoRNAs. Other snoRNA genes are found in polycistronic arrays, containing from two to seven snoRNA genes, a common organization for plant snoRNAs. Additionally, S. cerevisiae also has independently transcribed monocistronic box C/D snoRNA genes (3). The genomic organization of the box H/ACA snoRNAs is not as variable as that of the box C/D snoRNAs, and none are found within polycistronic transcripts. Almost all of them are monocistronic genes, though a couple are found within the introns of protein coding genes (6). In addition, while almost all of the snoRNA genes in S. cerevisiae are transcribed by RNA polymerase II, snR52 is transcribed by RNA polymerase III (13).
Last updated: 2007-06-29