Characterization and functional analysis of a novel double-guide C/D box snoRNA in the fission yeast

Biochemical and Biophysical Research Communications

Volumn 354, Issue 1, 2007, Pages 302-308

  Bi, Yan Zhen ^a   Qu, Liang Hu ^a   Zhou, Hui ^a  

^a BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

Author keywords

Methylation; Schizosaccharomyces pombe; snoRNA; snR88

Indexed keywords

FUNGAL RNA; RIBOSE; RIBOSOME RNA; RNA 25S; SMALL NUCLEOLAR RNA; UNCLASSIFIED DRUG; URIDINE;

ARTICLE; CELL VIABILITY; CONTROLLED STUDY; FUNGAL GENETICS; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENETIC ANALYSIS; KNOCKOUT GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION; RNA ANALYSIS; RNA GENE; RNA METHYLATION; RNA STRUCTURE; RNA SYNTHESIS; SCHIZOSACCHAROMYCES POMBE; SEQUENCE ANALYSIS; SNR88 GENE; TATA BOX;

BASE SEQUENCE; DNA METHYLATION; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS, GENETIC; RNA, SMALL NUCLEOLAR; SCHIZOSACCHAROMYCES;

EUKARYOTA; SCHIZOSACCHAROMYCES POMBE; SCHIZOSACCHAROMYCETACEAE;

EID: 33846315039     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2006.12.207     Document Type: Article

References (27)

1. Maden B.E.H. Mapping 2′-O-methyl groups in ribosomal RNA. Methods 25 (2001) 374-382
2. Bachellerie J.P., Cavaille J., and Huttenhofer A. The expanding snoRNA world. Biochimie 84 (2002) 775-790
3. Lestrade L., and Weber M.J. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res. 34 (2006) D158-D162
4. Uliel S., Liang X.H., Unger R., and Michaeli S. Small nucleolar RNAs that guide modification in trypanosomatids: repertoire, targets, genome organisation, and unique functions. Int. J. Parasitol. 34 (2004) 445-454
5. Huang Z.P., Zhou H., He H.L., Chen C.L., Liang D., and Qu L.H. Genome-wide analyses of two families of snoRNA genes from Drosophila melanogaster, demonstrating the extensive utilization of introns for coding of snoRNAs. RNA 11 (2005) 1303-1316
6. Zemann A., Bekke A.O.D., Kiefmann M., Brosius J., and Schmitz J. Evolution of small nucleolar RNAs in nematodes. Nucleic Acids Res. 34 (2006) 2676-2685
7. Russell A.G., Schnare M.N., and Gray M.W. A large collection of compact box C/D snoRNAs and their isoforms in Euglena gracilis: structural, functional and evolutionary insights. J. Mol. Biol. 357 (2006) 1548-1565
8. Brown J.W.S., Echeverria M., and Qu L.H. Plant snoRNAs: functional evolution and new modes of gene expression. Trends Plant Sci. 8 (2003) 42-49
9. Li S.G., Zhou H., Luo Y.P., Zhang P., and Qu L.H. Identification and functional analysis of 20 Box H/ACA small nucleolar RNAs (snoRNAs) from Schizosaccharomyces pombe. J. Biol. Chem. 280 (2005) 16446-16455
10. Omer A.D., Lowe T.M., Russell A.G., Ebhardt H., Eddy S.R., and Dennis P.P. Homologs of small nucleolar RNAs in Archaea. Science 288 (2000) 517-522
11. Jady B.E., and Kiss T. Characterisation of the U83 and U84 small nucleolar RNAs: two novel 2′-O-ribose methylation guide RNAs that lack complementarities to ribosomal RNAs. Nucleic Acids Res. 28 (2000) 1348-1354
12. Kishore S., and Stamm S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311 (2006) 230-232
13. Kiss-Laszlo Z., Henry Y., and Kiss T. Sequence and structural elements of methylation guide snoRNAs essential for site-specific ribose methylation of pre-rRNA. EMBO J. 17 (1998) 797-807
14. Kiss-Laszlo Z., Henry Y., Bachellerie J.P., Caizergues-Ferrer M., and Kiss T. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85 (1996) 1077-1088
15. Yang J.H., Zhang X.C., Huang Z.P., Zhou H., Huang M.B., Zhang S., Chen Y.Q., and Qu L.H. snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome. Nucleic Acids Res. 34 (2006) 5112-5123
16. Yu Y.T., Shu M.D., and Steiz J.A. A new method for detecting sites of 2′-O-methylation in RNA molecules. RNA 3 (1997) 324-331
17. Wach A., Brachat A., Pohlmann R., and Philippsen P. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10 (1994) 1793-1808
18. Gietz D., Jean A.S., Woods R.A., and Schiestl R.H. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 25 (1992) 1425
19. Chomczynski P., and Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162 (1987) 156-159
20. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res.31 31 (2003) 3406-3415
21. Lowe T.M., and Eddy S.E. A computational screen for methylation guide snoRNAs in yeast. Science 283 (1999) 1168-1171
22. ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Intron_Data/.
23. Maden B.E.H., Corbett M.E., Heeney P.A., Pugh K., and Ajuh P.M. Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA. Biochimie 77 (1995) 22-29
24. Davis D.R. Biophysical and conformational properties of modified nucleotides in RNA (nuclear magnetic resonance studies). In: Grosjean H., and Benne R. (Eds). Modification and Editing of RNA (1998), American Society of Microbiology Press, Washington, DC 85-102
25. Blanchard S.C., and Puglisi J.D. Solution structure of the A loop of 23S ribosomal RNA. PNAS 98 (2001) 3720-3725
26. Kehrenberg C., Schwarz S., Jacobsen L., Hansen L.H., and Vester B. A new mechanism for chloramphenicol, florfenicol and clindamycin resistance: methylation of 23S ribosomal RNA at A2503. Mol. Microbiol. 57 (2005) 1064-1073
27. Rein A., Henderson L.E., and Levin J.G. Nucleic-acid-chaperone activity of retroviral nucleocapsid proteins: significance for viral replication. Trends Biochem. Sci. 23 (1998) 297-301