Identification of six new box C/D snoRNA gene clusters from rice

IUBMB Life

Volumn 59, Issue 10, 2007, Pages 664-674

  Li, Wei ^a   Jiang, Ge ^a   Zeng, Dabo ^a   Jin, Youxin ^a  

^a INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

Author keywords

2 O ribose methylation; Box C D snoRNA; Plant; Rice

Indexed keywords

RIBOSOME RNA; SMALL NUCLEOLAR RNA;

ARTICLE; CONTROLLED STUDY; GENE CLUSTER; GENE IDENTIFICATION; GENETIC TRANSCRIPTION; METHYLATION; NONHUMAN; NUCLEOTIDE SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RICE; YEAST;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; GENES, PLANT; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; ORYZA SATIVA; RNA, PLANT; RNA, RIBOSOMAL; RNA, SMALL NUCLEOLAR; TRANSCRIPTION, GENETIC; ZEA MAYS;

ARABIDOPSIS THALIANA; ORYZA SATIVA;

EID: 34648831492     PISSN: 15216543     EISSN: 15216551     Source Type: Journal    
DOI: 10.1080/15216540701589312     Document Type: Article

References (47)

1. Maxwell, E. S., and Fournier, M. J. (1995) The small nucleolar RNAs. Annu. Rev. Biochem. 64, 897-934.
2. Balakin, A. G., Smith, L., and Fournier, M. J. (1996) The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell 86, 823-834.
3. Tollervey, D., and Kiss, T. (1997) Function and synthesis of small nucleolar RNAs. Curr. Opin. Cell Biol. 3, 337-342.
4. Watkins, N. J., Segault, V., Charpentier, B., Nottrott, S., Fabrizio, P., Bachi, A., Wilm, M., Rosbash, M., Branlant, C., and Luhrmann R. (2000)A common core RNP structure shared between the small nucleolar box C/D RNPs and the spliceosomal U4 snRNP. Cell 103, 457-466.
5. Kiss-Laszlo, Z., Henry, Y., Bachellerie, J. P., Caizergues-Ferrer, M., and Kiss, T. (1996) Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85, 1077-1088.
6. Watkins, N. J., Gottschalk, A., Nwubauer, G., Kastner, B., Fabrizio, P., Mann, M., and Luhrmann, R. (1998) Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H BOX/ACA-motif snoRNAs and constitute a common bipartite structure. RNA 4, 1549-1568.
7. Tycowski, K. T., You, Z. H., Graham, P. J., and Steitz, J. A. (1998) Modification of U6 spliceosomal RNA is guided by other small RNAs. Mol. Cell 2, 629-638.
8. Huttenhofer, A., Kiefmann, M., Meier-Ewert, S., O'Brien, J., Lehrach, H., Bachellerie, J. P., and Brosius, J. (2001) Rnomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO J. 20, 2943-2953.
9. Darzacq, X., Jady, B. E., Verheggen, C., Kiss, A. M., Bertrand, E., and Kiss, T. (2002) Cajal body-specific small nuclear RNAs: a novel class of 2′-O-methylation and pseudouridylation guide RNAs. EMBO J. 21, 2746-2756.
10. Li, W., Jiang, G., Huang, B., and Jin, Y. X. (2005) A novel snoRNA can direct site-specific 2′-O-ribose methylation of snRNAs in Oryza sativa. IUBMB Life 57,173-179.
11. Clouet d'Orval, B., Bortolin, M. L., Gaspin, C., and Bachellerie, J. P. (2001) Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp. Nucleic Acids Res. 29, 4518-4529.
12. Renalier, M. H., Joseph, N., Gaspin, C., Thebault, P., and Mougin, A. (2005) The Cm56 tRNA modification in archaea is catalyzed either by a specific 2′-O-methylase, or a C/D sRNP. RNA 11, 1051-1063.
13. Vitali, P., Basyuk, E., Le Meur, E., Bertrand, E., Muscatelli, F., Cavaille, J., and Huttenhofer, A. (2005) ADAR2-mediated editing of RNA substrates in the nucleolus is inhibited by C/D small nucleolar RNAs. J. Cell Biol. 169, 745-753.
14. Kishore, S., and Stamm, S. (2006) The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311(5758), 230-232.
15. Smith, C. M., and Steiz, J. A. (1997) Sno storm in the nucleolus: new roles for myriad small RNPs. Cell 89, 669-672.
16. Omer, A. D., Lowe, T. M., Russell, A. G., Ebhardt, H., Eddy, S. R., and Dennis, P. P. (2000) Homologs of small nucleolar RNAs in Archaea. Science 288, 991-994.
17. Tang, T. H., Bachellerie, J. P., Rozhdestvensky, T., Bortolin, M. L., Huber, H., Drungowski, M., Elge, T., Brosius, J., and Huttenhofer, A. (2002) Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc. Natl. Acad. Sci. 99, 7536-7541.
18. Yuan, G. Z., Klambt, C., Bachellerie, J. P., Brosius, J., and Huttenhofer, A. (2003) RNomics in Drosophila melanogaster: identification of 66 candidates for novel non-messenger RNAs. Nucleic Acids Res. 31, 2495-2507.
19. Liang, X. H., Ochaion A., Xu, Y. X., Liu, Q., and Michaeli, S. (2004) Small nucleolar RNA clusters in Trypanosomatid Leptomonas collosoma. Genome organization, expression studies, and the potential role of sequences present upstream from the first repeated cluster. J. Biol. Chem. 279, 5100-5109.
20. Yang, C. Y., Zhou, H., Luo, J., and Qu, L. H. (2005) Identification of 20 snoRNA-like RNAs from the primitive eukaryote, Giardia lamblia. Biochem. Biophys. Res. Commun. 328, 1224-1231.
21. Russell, A. G., Schnare, M. N., and Gray, M. W. (2006) A large collection of compact box C/D snoRNAs and their isoforms in Euglena gracilis: structural, functional and evolutionary insights. J. Mol. Biol. 357, 1548-1565.
22. Aspegren, A., Hinas, A., Larsson, P., Larsson, A., and Soderbom, F. (2004) Novel non-coding RNAs in Dictyostelium discoideum and their expression during development. Nucleic Acids Res. 32, 4646-4656.
23. Cecchini, J. P., and Miassod, R. (1979) Studies on the methylation of cytoplasm RNA from cultured higher plant cells. Eur. J. Biochem. 98, 203-214.
24. Brown, J. W. S., Echeverria, M., and Qu, L. H. (2003) Plant snoRNAs: functional evolution and new modes of gene expression. Trends Plant Sci. 8, 42-49.
25. Chen, C. L., Liang, D., Zhou, H., Zhuo, M., Chen, Y. Q., and Qu, L. H. (2003) The high diversity of snoRNAs in plants: identification and comparative study of 120 snoRNA genes from Oryza sativa. Nucleic Acids Res. 31, 2601-2613.
26. Leader, D. J., Clark, G. P., Waters, J., Beven, A. F., Shaw, P. J., and Brown, J. W. S. (1997) Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic pre-snoRNAs. EMBO J. 16, 5742-5751.
27. Qu, L. H., Meng, Q., Zhou, H., and Chen, Y. Q. (2001) Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana. Nucleic Acids Res. 29, 1623-1630.
28. Barneche, F., Gaspin, C., Guyot, R., and Echeverria, M. (2001) Identification of 66 box C/D snoRNAs in Arabidopsis thaliana duplications generated multiple isoforms predicting new RNA 2′-O-methylation sites. J. Mol. Biol. 3, 57-73.
29. Brown, J. W. S., Clark, G. P., Leader, D. J., Simpson, C. G., and Lowe, T. (2001) Multiple snoRNA gene clusters from Arabidopsis. RNA 7, 1817-1832.
30. Marker, C., Zemann, A., Terhorst, T., Kiefmann, M., Kastenmayer, J. P., Green, P., Bachellerie, J. P., Brosius, J., and Huttenhofer, A. (2002) Experimental Rnomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana. Curr Biol. 12, 2002-2013.
31. Brown, J. W. S., Echeverria, M., Qu, L. H., Lowe, T. M., Bachellerie, J. P., Huttenhofer, A., Kastenmayer, J. P., Green, P. J., Shaw, P., and Marshall, D. F. (2003) Plant snoRNA database. Nucleic Acids Res. 31, 432-435.
32. Jiang, G., Chen, X. L., Li, W., Jin, Y. X., and Wang, D. B. (2002) Identification and characterization of novel U14 snoRNA gene cluster in Oryza sativa. Gene 294, 187-196.
33. Liang, D., Zhou, H., Zhang, P., Chen, Y. Q., Chen, X., Chen, C. L., and Qu, L. H. (2002) A novel gene organization: intronic snoRNA gene clusters from Oryza sativa. Nucleic Acids Res. 30, 3262-3272.
34. Kiss, T., and Filipowicz, W. (1995) Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns. Genes Dev. 9, 1411-1424.
35. Tycowski, K. T., Aab, A., and Steitz, J. A. (2004) Guide RNAs with 5′ caps and novel box C/D snoRNA-like domains for modification of snRNAs in metazoa. Curr. Biol. 14, 1985-1995.
36. Qu, L. H., Zhong, L., Shi, S., Lu, Y., Zhou, H., Fang, R., and Wang, Q. (1997) Two snoRNAs are encoded in the first intron of the rice hsp70 gene. Prog Natural Sci. 7, 371-377.
37. Kruszka, K., Barneche, F., Guyot, R., Ailhas, J., Meneau, I., Schiffer, S., Marchfelder, A., and Echeverria, M. (2003) Plant dicistronic tRNA-snoRNA genes: a new mode of expression of the small nucleolar RNAs processed by RNase Z. EMBO J. 3, 621-632.
38. Li, W., Jiang, G., Jin, Y. X., and Wang, D. B. (2003) Detection of 2′-O-ribose methylation sites on rice 25 S rRNA. Acta Bioch. Bioph. Sin. 35, 289-295.
39. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidmen, J. G., Smith, J. A., and Struhl, K. (1995) Current Protocols in Molecular Biology, 3rd edn, John Wiley & sons, Inc, New York.
40. Lessard, P., Decroocq, V., and Thomas, M. (1997) Isolation and analysis of messenger RNA from plant cells cloning of cDNAs. In Plant Molecular Biology: A Laboratory Manual (Melody, S. C., ed.), pp. 154-198. Springer-Verlag, Berlin, Heidelberg.
41. Lowe, T. M., and Eddy, S. R. (1999) A computational screen for methylation guide snoRNAs in yeast. Science 283, 1168-1171.
42. Cavaille, J., Nicoloso, M., and Bachellerie, J. P. (1996) Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature 24, 732-735.
43. Brown, J. W. S., and Shaw, P. J. (1998) Small nucleolar RNAs and pre-rRNA processing in plants. Plant Cell 10, 649-657.
44. Zagorski, J., Tollervey, D., and Fournier, M. J. (1988) Characterization of an SNR Gene Locus in Saccharomyces cerevisiae that specifies both dispensable and essential small nuclear RNAs. Biol. Mol. Cell Biol. 8, 3282-3290.
45. Qu, L. H., Henras, A., Lu, Y. J., Zhou, H., Zhou, W. X., Zhu, Y. Q., Zhao, J., Henry, Y., Caizergues-Ferrer, M., and Bachellerie, J. P. (1999) Seven novel methylation guide small nucleolar RNAs are processed from a common polycistronic transcript by Rat1p and Rnase III in yeast. Mol. Cell Biol. 19, 1144-1158.
46. Leader, D. J., Clark, G. P., Waters, J., Beven, A. F., Shaw, P. J., and Brown, J. W. S. (1999) Splicing-independent processing of plant box C/D and box H/ACA small nucleolar RNAs. Plant Mol. Biol. 39, 1091-1100.
47. Lawrence, J. (1999) Selfish operons: The evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9, 642-648.