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HUGO Gene Nomenclature Committee
HGNC Approved SymbolHGNC Approved Name
SNORD3@small nucleolar RNA, C/D box 3 cluster
snoid : SR0000239
Length : 217
Abstract : Homo sapiens C/D box U3 snoRNA. The U3 snoRNA is found in many organisms. Human U3 from HeLa cells was sequenced by Nohga et al. (1981) and cloned from HeLa cells extracts precipitated with anti-(U3)RNP and anti-TMG antibodies by Tyc and Steitz (1989). In yeast, mouse and Xenopus, U3 is required for the maturation of 18S rRNA (Savino et al., 1990; Kass et al., 1990, Borovjagin and Gerbi, 1999, 2000, 2001, 2004). It is transcribed from independent RNA polII transcription units, possess a trimethylguanosine cap and is localized in the nucleolus. U3 is associated in a 12S RNP with the four core proteins of C/D box snRNPs, plus a U3-specific protein, RNU3IP2 (hU3-55K ), the human orthologue of yeast Rrp9p (Lübben et al., 1993; Pluk et al., 1998). The snRNA U3 is also present in the ~80S pre-rRNA processing complex (Granneman et al., 2004 and ref. therein), where it associates with additional proteins, including MPHOSPH10 (hMpp10, Westendorf et al. 1998), IMP3 and IMP4 (Granneman et al., 2003). In the yeast S. cerevisiae, the disruption of U3 RNA leads to the loss of the 5' terminal knobs (SSU processome) of pre-rRNA transcripts (Dragon et al., 2002). In interphase human cells, genes encoding U3 snoRNAs are frequently associated with Cajal bodies, as previously shown for U1, U2 and histone genes (Gao et al., 1997). The 3' end processing of U3, cap hypermethylation by PIMT (hTgs1) and assembly of U3 snoRNA take place in Cajal bodies (Verheggen et al., 2002). U3 is composed of a 5' domain, with conserved sequences CAG box, A' and A boxes, 5' and 3' hinges, and a 5' domain with conserved C', B, C and D boxes. In the 5' domain, boxes A' and A form conserved base-pair interactions with 18S rRNA (Hughes, 1996). The 5' and 3' hinges of the 5' domain form base-pair interactions with nts 1408-1416 and 438-444, respectively, of the pre-rRNA 5' ETS (Borovjagin and Gerbi, 2000). The later sequence in the 5'ETS is located near the evolutionary conserved motive (ECM, nts 420 -432) that contains the UCGA binding sequence of nucleolin, a protein required to load U3 snoRNA on the 5'ETS (Ginisty et al., 1998, 2000). The human genome contains 5 U3-related genes clustered on chr17p11.2: one copy of each U3, U3-3 and U3-4, and two copies of U3-2. None is identical to the U3a and U3b sequences published by Gao et al. (1997). From their restriction maps, U3b would correspond to U3-2, and U3a to U3-4. Compared to the 4 other copies of U3, the 5' domain of U3-4 contains two mutations, one of which in the conserved GAC box.
GenBank accession number : X14945
Host gene : Independent transcriptional unit
Click here to see the position on the UCSC Genome Browser
Target RNA : unknown
References :
- Nohga, K., Reddy, R., and Busch, H. (1981). Comparison of RNase T1 fingerprints of U1, U2, and U3 small nuclear RNA's of HeLa cells, human normal c 41, 2215-2220.
- Lübben, B., Marshallsay, C., Rottmann, N., and Luhrmann, R. (1993). Isolation of U3 snoRNP from CHO cells: a novel 55 kDa protein binds to the central part of U3 snoRNA. Nucleic Acids Res, 21, 5377-5385.
- Pluk, H., Soffner, J., Luhrmann, R., and van Venrooij, W. J. (1998). cDNA cloning and characterization of the human U3 small nucleolar ribonucleoprotein complex-associated 55-kilodalton protein. Mol Cell Biol, 18, 488-498.
- Westendorf, J. M., Konstantinov, K. N., Wormsley, S., Shu, M. D., Matsumoto-Taniura, N., Pirollet, F., Klier, F. G., Gerace, L., and Baserga, S. J. (1998). M phase phosphoprotein 10 is a human U3 small nucleolar ribonucleoprotein component. Mol Biol Cell, 9, 437-449.
- Granneman, S., Gallagher, J. E., Vogelzangs, J., Horstman, W., van Venrooij, W. J., Baserga, S. J., and Pruijn, G. J. (2003). The human Imp3 and Imp4 proteins form a ternary complex with hMpp10, which only interacts with the U3 snoRNA in 60-80S ribonucleoprotein complexes. Nucleic Acids Res, 31, 1877-1887.
- Granneman, S., Vogelzangs, J., Luhrmann, R., van Venrooij, W. J., Pruijn, G. J., and Watkins, N. J. (2004). Role of pre-rRNA base pairing and 80S complex formation in subnucleolar localization of the U3 snoRNP. Mol Cell Biol, 24, 8600-8610.
- Savino, R., and Gerbi, S. A. (1990). In vivo disruption of Xenopus U3 snRNA affects ribosomal RNA processing. Embo J, 9, 2299-2308.
- Kass, S., Tyc, K., Steitz, J. A., and Sollner-Webb, B. (1990). The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing. Cell, 60, 897-908.
- Borovjagin, A. V., and Gerbi, S. A. (1999). U3 small nucleolar RNA is essential for cleavage at sites 1, 2 and 3 in pre-rRNA and determines which rRNA processing pathway is taken in Xenopus oocytes. J Mol Biol, 286, 1347-1363.
- Borovjagin, A. V., and Gerbi, S. A. (2000). The spacing between functional cis-elements of U3 snoRNA is critical for rRNA processing. J Mol Biol, 300, 57-74.
- Borovjagin, A. V., and Gerbi, S. A. (2001). Xenopus U3 snoRNA GAC-Box A' and Box A sequences play distinct functional roles in rRNA processing. Mol Cell Biol, 21, 6210-6221.
- Borovjagin, A. V., and Gerbi, S. A. (2004). Xenopus U3 snoRNA docks on pre-rRNA through a novel base-pairing interaction. Rna, 10, 942-953.
- Hughes, J. M. (1996). Functional base-pairing interaction between highly conserved elements of U3 small nucleolar RNA and the small ribosomal subunit RNA. J Mol Biol, 259, 645-654.
- Ginisty, H., Amalric, F., and Bouvet, P. (1998). Nucleolin functions in the first step of ribosomal RNA processing. Embo J, 17, 1476-1486.
- Ginisty, H., Serin, G., Ghisolfi-Nieto, L., Roger, B., Libante, V., Amalric, F., and Bouvet, P. (2000). Interaction of nucleolin with an evolutionarily conserved pre-ribosomal RNA sequence is required for the assembly of the primary processing complex. J Biol Chem, 275, 18845-18850.
- Tyc, K., and Steitz, J. A. (1989). U3, U8 and U13 comprise a new class of mammalian snRNPs localized in the cell nucleolus. Embo J, 8, 3113-3119.
- Verheggen, C., Lafontaine, D. L., Samarsky, D., Mouaikel, J., Blanchard, J. M., Bordonne, R., and Bertrand, E. (2002). Mammalian and yeast U3 snoRNPs are matured in specific and related nuclear compartments. Embo J, 21, 2736-2745.
- Gao, L., Frey, M. R., and Matera, A. G. (1997). Human genes encoding U3 snRNA associate with coiled bodies in interphase cells and are clustered on chromosome 17p11.2 in a complex inverted repeat structure. Nucleic Acids Res, 25, 4740-4747.
- Dragon, F., Gallagher, J. E., Compagnone-Post, P. A., Mitchell, B. M., Porwancher, K. A., Wehner, K. A., Wormsley, S., Settlage, R. E., Shabanowitz, J., Osheim, Y., et al. (2002). A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature, 417, 967-970.
Sequence :
Phylogenic conservation: Alignment - Fasta file
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