Small nucleolar RNA U3

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Metazoan U3 secondary structure.png
Metazoan U3 RNA secondary structure and sequence conservation
Symbol U3
Alt. Symbols RNU3P2,
Rfam RF00012
Entrez 26844
HUGO 10176
OMIM 180710
Other data
RNA type snoRNA
Domain(s) Eukaryota;
SO {{{SO}}}
PDB structures PDBe

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]

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[edit]

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[edit]


  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" (Free full text). 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&ndash, 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&ndash, 8421. 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. doi:10.4161/rna.6.5.9607. PMID 19875933.

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