Small nucleolar RNA U3

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U3
Metazoan U3 secondary structure.png
Metazoan U3 RNA secondary structure and sequence conservation
Identifiers
SymbolU3
Alt. SymbolsRNU3P2,
Rfam RF00012
NCBI Gene 26844
HGNC 10176
OMIM 180710
Other data
RNA type snoRNA
Domain(s) Eukaryota;
PDB structures PDBe

In molecular biology, U3 snoRNA is a non-coding RNA found predominantly in the nucleolus. U3 has C/D box motifs that technically make it a member of the box C/D class of snoRNAs; however, unlike other C/D box snoRNAs, it has not been shown to direct 2'-O-methylation of other RNAs. Rather, U3 is thought to guide site-specific cleavage of ribosomal RNA (rRNA) during pre-rRNA processing. [1]

Contents

The box C/D element is a subset of the six short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C, C', and D. [2] The U3 snoRNA secondary structure is characterized by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hyper-methylation of U3 snoRNA. [3] Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.

Species-specific secondary structure models

S. cerevisiae secondary structure determined by chemical mapping of U3A RNA in a purified snoRNP is available. [4] A human structure model has also been proposed. [5] Like yeast and human, protozoan protist Entamoeba histolytica : a primitive eukaryote adopted the same conserved secondary structure of U3 snoRNA. [6] Four consensus structures specific to metazoa, fungi, plants and basal eukaryotes have been proposed. [7]

See also

Related Research Articles

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Small nucleolar RNA snoR1

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Small nucleolar RNA SNORD82

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In molecular biology, snoR9 is a non-coding RNA (ncRNA) which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). It is known as a small nucleolar RNA (snoRNA) and also often referred to as a 'guide RNA'.

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NOP58

Nucleolar protein 58 is a protein that in humans is encoded by the NOP58 gene.

Nucleolar protein, member A1

H/ACA ribonucleoprotein complex subunit 1 is a protein that in humans is encoded by the GAR1 gene.

RRP9

U3 small nucleolar RNA-interacting protein 2 is a protein that in humans is encoded by the RRP9 gene.

Small nucleolar RNA sR8 world of history

In molecular biology, Small nucleolar RNA sR8 is a non-coding RNA belonging to the C/D box class of snoRNAs. sR8, along with other C/D box snoRNAs, performs 2′-O-methylation of ribose on a target strand of ribosomal RNA. Targeting is achieved through the C and D box components, which are short sections of conserved sequences, as well as C'/D' boxes. These sequences base-pair with nucleotides in the target rRNA to direct their methylation.

References

  1. ↑ Cléry, A.; Senty-Ségault, V.; Leclerc, F.; Raué, A.; Branlant, C. (Feb 2007). "Analysis of sequence and structural features that identify the B/C motif of U3 small nucleolar RNA as the recognition site for the Snu13p-Rrp9p protein pair". Molecular and Cellular Biology. 27 (4): 1191–1206. doi:10.1128/MCB.01287-06. ISSN   0270-7306. PMC   1800722 . PMID   17145781.
  2. ↑ Zwieb, C (1997). "The uRNA database". Nucleic Acids Res. 25 (1): 102–103. doi:10.1093/nar/25.1.102. PMC   146409 . PMID   9016512.
  3. ↑ Speckmann, W; Narayanan A; Terns R; Terns MP (1999). "Nuclear retention elements of U3 small nucleolar RNA". Mol Cell Biol. 19 (12): 8412–8421. doi:10.1128/MCB.19.12.8412. PMC   84939 . PMID   10567566.
  4. ↑ Méreau A, Fournier R, Grégoire A, et al. (October 1997). "An in vivo and in vitro structure-function analysis of the Saccharomyces cerevisiae U3A snoRNP: protein-RNA contacts and base-pair interaction with the pre-ribosomal RNA". J. Mol. Biol. 273 (3): 552–71. doi:10.1006/jmbi.1997.1320. PMID   9356246.
  5. ↑ Granneman S, Vogelzangs J, Lührmann R, van Venrooij WJ, Pruijn GJ, Watkins NJ (October 2004). "Role of pre-rRNA base pairing and 80S complex formation in subnucleolar localization of the U3 snoRNP". Mol. Cell. Biol. 24 (19): 8600–10. doi:10.1128/MCB.24.19.8600-8610.2004. PMC   516741 . PMID   15367679.
  6. ↑ Srivastava A, Ahamad J, Ray AK, Kaur D, Bhattacharya A, Bhattacharya S (2014). Analysis of U3 snoRNA and small subunit processome components in the parasitic protist Entamoeba histolytica. Mol Biochem Parasitol. 193(2):82-92. doi: 10.1016/j.molbiopara.2014.03.001. Epub 2014 Mar 12
  7. ↑ Marz M, Stadler PF (2009). "Comparative analysis of eukaryotic U3 snoRNA". RNA Biol. 6 (5): 503–7. CiteSeerX   10.1.1.380.4189 . doi:10.4161/rna.6.5.9607. PMID   19875933. S2CID   13055120.


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