SNR53/snR53 Summary Help

Standard Name SNR53 1
Systematic Name snR53
Feature Type snoRNA
Description C/D box small nucleolar RNA (snoRNA); guides 2'-O-methylation of small subunit (SSU) rRNA at position A796 (1, 2, 3 and see Summary Paragraph)
Name Description Small Nucleolar RNA 1
Chromosomal Location
ChrV:61699 to 61789 | ORF Map | GBrowse
Gbrowse
Gene Ontology Annotations All SNR53 GO evidence and references
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 1 genes
Resources
Classical genetics
null
sequence information
ChrV:61699 to 61789 | ORF Map | GBrowse
SGD ORF map
Last Update Coordinates: 2000-05-19 | Sequence: 2000-05-19
Subfeature details
Relative
Coordinates
Chromosomal
Coordinates
Most Recent Updates
Coordinates Sequence
Noncoding exon 1..91 61699..61789 2000-05-19 2000-05-19
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
Resources
External Links All Associated Seq | Search all NCBI (Entrez) | snoRNA database at UMass Amherst
Primary SGDIDS000006444
SUMMARY PARAGRAPH for SNR53

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 (3, 4). 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 (5) 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 (4, 5). 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 (6): Nop1p (the homolog of vertebrate fibrillarin, 7), 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 (3, 8, 9). 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 (6). 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 (1). 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 (8). It is notable that the sites of modification are in functionally important regions and many are conserved across species (3, 10). In mammals, snRNAs involved in mRNA splicing are also methylated and mRNAs may also be methylated by box C/D snoRNPs with regulatory consequences (10).

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 (3, 9). 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 (3, 9). The snR10 snoRNA is not essential and its deletion produces only a mild reduction in 18S rRNA accumulation (9). U14 and snR10 are involved in both endonucleolytic cleavage steps and in targeting RNA modification reactions (9). 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 (9).

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 (1). 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 (3). 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 (11).

Last updated: 2007-06-29 Contact SGD

References cited on this page View Complete Literature Guide for SNR53
1) Lowe TM and Eddy SR  (1999) A computational screen for methylation guide snoRNAs in yeast. Science 283(5405):1168-71
2) Samarsky DA and Fournier MJ  (1999) A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae. Nucleic Acids Res 27(1):161-4
3) Piekna-Przybylska D, et al.  (2007) New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA 13(3):305-12
4) Tollervey D and Kiss T  (1997) Function and synthesis of small nucleolar RNAs. Curr Opin Cell Biol 9(3):337-42
5) Reichow SL, et al.  (2007) The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res 35(5):1452-64
6) Galardi S, et al.  (2002) Purified box C/D snoRNPs are able to reproduce site-specific 2'-O-methylation of target RNA in vitro. Mol Cell Biol 22(19):6663-8
7) Schimmang T, et al.  (1989) A yeast nucleolar protein related to mammalian fibrillarin is associated with small nucleolar RNA and is essential for viability. EMBO J 8(13):4015-24
8) Venema J and Tollervey D  (1996) RRP5 is required for formation of both 18S and 5.8S rRNA in yeast. EMBO J 15(20):5701-14
9) Venema J and Tollervey D  (1999) Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet 33:261-311
10) Fatica A and Tollervey D  (2003) Insights into the structure and function of a guide RNP. Nat Struct Biol 10(4):237-9
11) Moqtaderi Z and Struhl K  (2004) Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol Cell Biol 24(10):4118-27