SNR17A/snR17a Summary Help

Standard Name SNR17A 1
Systematic Name snR17a
Feature Type snoRNA
Description Small nucleolar RNA (snoRNA) U3; part of Small ribosomal SubUnit (SSU) processosome; SNR17B also encodes snoRNA U3 (see Summary Paragraph)
Name Description Small Nucleolar RNA
Gene Product Alias U3 1
Chromosomal Location
ChrXV:780107 to 780596 | ORF Map | GBrowse
Gbrowse
Genetic position: 136 cM
Gene Ontology Annotations All SNR17A GO evidence and references
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
High-throughput
Regulators 5 genes
Resources
Classical genetics
null
25 total interaction(s) for 24 unique genes/features.
Physical Interactions
  • Affinity Capture-RNA: 23
  • Co-fractionation: 2

sequence information
ChrXV:780107 to 780596 | ORF Map | GBrowse
SGD ORF map
Genetic position: 136 cM
Last Update Coordinates: 2011-02-03 | Sequence: 2000-05-19
Subfeature details
Relative
Coordinates
Chromosomal
Coordinates
Most Recent Updates
Coordinates Sequence
Noncoding exon 1..14 780107..780120 2011-02-03 2000-05-19
Intron 15..171 780121..780277 2011-02-03 2000-05-19
Noncoding exon 172..490 780278..780596 2011-02-03 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 SGDIDS000007294
SUMMARY PARAGRAPH for SNR17A

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 (2, 3). 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 (4) For a complete listing of all the snoRNA genes in S cerevisiae, see the table of snoRNAs.

About the U3 snoRNA

The U3 snoRNA is one of the most abundant RNA molecules in S. cerevisiae, present at about 400-1000 copies per cell (1). U3 is a box C/D snoRNA (3) encoded by two genes, snR17A and snR17B, both of which contain an intron with an atypical branch point sequence (5). Both U3 genes are transcribed, though snR17A is 5-10 fold more abundant than snR17B (1, 5). Each is 328 nucleotides long and they are 96% identical in the region of the mature RNA (1). U3 from S. cerevisiae is over 100 nucleotides longer than U3 from most other eukaryotes, e.g. human, rat, or dictystelium, but shares conserved primary and secondary structure elements (1), including perfect complementarity to a conserved sequence within the 5'-ETS of the primary rRNA transcript(6) and to three highly conserved sequences within the 18S rRNA which form the conserved pseudoknot found at the core of all small subunit rRNAs (7). While either snR17A or snR17B can be deleted without any effect, the double deletion is inviable, indicating that U3 is essential (1).

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 (3, 4). 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 (8): Nop1p (the homolog of vertebrate fibrillarin, 9), 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 (2, 10, 11). 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 (8). 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 (12). 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 (10). It is notable that the sites of modification are in functionally important regions and many are conserved across species (2, 13). In mammals, snRNAs involved in mRNA splicing are also methylated and mRNAs may also be methylated by box C/D snoRNPs with regulatory consequences (13).

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 (2, 11). 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 (2, 11). The snR10 snoRNA is not essential and its deletion produces only a mild reduction in 18S rRNA accumulation (11). U14 and snR10 are involved in both endonucleolytic cleavage steps and in targeting RNA modification reactions (11). 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 (11).

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 (12). 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 (2). 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 (14).

About the early stages of rRNA processing and 40S small ribosomal subunit assembly

The early stages of ribosome assembly occur in conjunction with processing of the 35S pre-ribosomal RNA transcript into the mature 18S, 5.8S, and 25S rRNA molecules. The first three cleavages at A0, A1, and A2 (see diagram) are essential for production of the 18S rRNA and the 40S small ribosomal subunit, but mutations which interfere with these cleavages have little effect on production of the 60S large ribosomal subunit (11). These three early cleavages occur in a series of large U3-associated ribonucleoprotein complexes (15, 16) and require base pairing of the U3 snoRNA with sequences in the 5'-ETS and the 18S rRNA (6, 7).

Click on the following figure for more details about the rDNA repeat and cleavage sites within the rRNA transcript:

figure 1

About the 90S preribosome and SSU processome complexes

A number of U3-containing early ribosome assembly and rRNA processing complexes have been identified that contain the 35S pre-rRNA transcript and have overlapping but not identical protein compositions (15, 16). Both the 90S preribosome and the small subunit (SSU) processome complexes contain ribosomal proteins, primarily of the small subunit, and non-ribosomal proteins presumably involved in rRNA processing and assembly of the small 40S ribsomal subunit. While many proteins are found in both complexes, some are found in only one or the other (see lists below). It may be that the 90S preribosome and SSU processome complexes are both intermediates in a series of complexes leading to the assembly of the small ribosomal subunit (15), or it may be that the SSU processome lies on an alternate assembly pathway (16).

The 90S preribosome complex is described as corresponding to the earliest detectable rRNA processing and ribosome assembly complex (17). The 90S is itself assembled from a number of stable subcomplexes including the t-UTP subcomplex (Utp5p, Utp4p, Nan1p, Utp8p, Utp9p, Utp10p, and Utp15p), the Pwp2p/UTP-B subcomplex (Utp6p, Pwp2p, Utp18p, Utp21p, Utp13p, and Dip2p) which interacts directly with the 5'-ETS of the 35S pre-rRNA (18), the UTP-C subcomplex (Rrp7p, Utp22p, Ckb1p, Cka1p, Ckb2p, and Cka2p), and the Mpp10 subcomplex (Mpp10p, Imp3p, and Imp4p) (19). The t-UTP subcomplex is also found as part of the SSU processome complex, which is slightly smaller at 80S (20, 21). Depletion of any of the members of the t-UTP subcomplex results in decreased transcription of rDNA leading to decreased levels of the primary 35S rRNA transcript (22). In contrast, mutation or depletion of most other members of either the 90S preribosome or SSU processome complexes causes decreased 18S rRNA levels without affecting the levels of the 25S or 5.8S rRNAs.

Non-ribosomal protein components of the 90S preribosome and SSU processome

Subunits of both the 90S preribosome (17) and SSU processome (20, 21) include: Bud21p, Dip2p, Ecm16p, Emg1p, Imp3p, Imp4p, Krr1p, Mpp10p, Nan1p, Noc4p, Nop1p, Nop14p, Nop58p, Pwp2p, Rrp5p, Rrp9p, Nop56p, Sof1p, Utp4p, Utp6p, Utp7p, Utp8p, Utp9p, Utp10p, Utp13p, Utp15p, Utp18p, Utp20p, Utp21p, and Utp22p

Additional subunits of the 90S preribosome (17) include: Bfr2p, Bms1p, Cbf5p, Cms1p, Dbp8p, Dim1p, Enp1p, Enp2p, Has1p, Kre33p, Mrd1p, Nop9p (23), Pno1p, Prp43p, Rcl1p, Rok1p, Rrp12p, Scl1p, Slx9p (24), Tsr1p, and Utp30p

Additional subunits of the SSU processome (20, 21) include: Fcf1p, Utp23p, Sas10p, Snu13p, Utp5p, Utp11p, and Utp14p

Last updated: 2007-06-29 Contact SGD

References cited on this page View Complete Literature Guide for SNR17A
1) Hughes JM, et al.  (1987) The yeast homologue of U3 snRNA. EMBO J 6(7):2145-55
2) Piekna-Przybylska D, et al.  (2007) New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA 13(3):305-12
3) Tollervey D and Kiss T  (1997) Function and synthesis of small nucleolar RNAs. Curr Opin Cell Biol 9(3):337-42
4) Reichow SL, et al.  (2007) The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res 35(5):1452-64
5) Myslinski E, et al.  (1990) An intron in the genes for U3 small nucleolar RNAs of the yeast Saccharomyces cerevisiae. Science 247(4947):1213-6
6) Beltrame M and Tollervey D  (1995) Base pairing between U3 and the pre-ribosomal RNA is required for 18S rRNA synthesis. EMBO J 14(17):4350-6
7) Hughes JM  (1996) Functional base-pairing interaction between highly conserved elements of U3 small nucleolar RNA and the small ribosomal subunit RNA. J Mol Biol 259(4):645-54
8) 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
9) 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
10) 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
11) Venema J and Tollervey D  (1999) Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet 33:261-311
12) Lowe TM and Eddy SR  (1999) A computational screen for methylation guide snoRNAs in yeast. Science 283(5405):1168-71
13) Fatica A and Tollervey D  (2003) Insights into the structure and function of a guide RNP. Nat Struct Biol 10(4):237-9
14) 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
15) Fromont-Racine M, et al.  (2003) Ribosome assembly in eukaryotes. Gene 313:17-42
16) Granneman S and Baserga SJ  (2004) Ribosome biogenesis: of knobs and RNA processing. Exp Cell Res 296(1):43-50
17) Grandi P, et al.  (2002) 90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors. Mol Cell 10(1):105-15
18) Dosil M and Bustelo XR  (2004) Functional characterization of Pwp2, a WD family protein essential for the assembly of the 90 S pre-ribosomal particle. J Biol Chem 279(36):37385-97
19) Perez-Fernandez J, et al.  (2007) The 90S preribosome is a multimodular structure that is assembled through a hierarchical mechanism. Mol Cell Biol 27(15):5414-29
20) Dragon F, et al.  (2002) A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature 417(6892):967-70
21) Bernstein KA, et al.  (2004) The small-subunit processome is a ribosome assembly intermediate. Eukaryot Cell 3(6):1619-26
22) Gallagher JE, et al.  (2004) RNA polymerase I transcription and pre-rRNA processing are linked by specific SSU processome components. Genes Dev 18(20):2506-17
23) Thomson E, et al.  (2007) Nop9 is an RNA binding protein present in pre-40S ribosomes and required for 18S rRNA synthesis in yeast. RNA 13(12):2165-2174
24) Bax R, et al.  (2006) Slx9p facilitates efficient ITS1 processing of pre-rRNA in Saccharomyces cerevisiae. RNA 12(11):2005-13