A combined computational and experimental analysis of two families of snoRNA genes from Caenorhabditis elegans, revealing the expression and evolution pattern of snoRNAs in nematodes

Genomics

Volumn 89, Issue 4, 2007, Pages 490-501

  Huang, Zhan Peng ^a   Chen, Chong Jian ^a   Zhou, Hui ^a   Li, Bei Bei ^a   Qu, Liang Hu ^a  

^a BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

Author keywords

Caenorhabditis elegans; Intron; ncRNA; RNA modification; snoRNA

Indexed keywords

COMPLEMENTARY RNA; SMALL NUCLEOLAR RNA; UNTRANSLATED RNA;

ARTICLE; CAENORHABDITIS ELEGANS; COILED BODY; COMPUTER ANALYSIS; CONTROLLED STUDY; EVOLUTIONARY HOMOLOGY; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE LOCATION; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC SCREENING; GENETIC VARIABILITY; GENOME ANALYSIS; HOMEOBOX; INTRON; MULTIGENE FAMILY; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; RNA GENE; RNA SPLICING; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SNORNA GENE;

ANIMALS; CAENORHABDITIS ELEGANS; GENOMICS; INTRONS; NEMATODA; RNA SPLICE SITES; RNA, SMALL NUCLEOLAR; SOFTWARE; VARIATION (GENETICS);

CAENORHABDITIS ELEGANS; EUKARYOTA; HEXAPODA; MAMMALIA; METAZOA; NEMATODA;

EID: 33947167823     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2006.12.002     Document Type: Article

References (45)

1. Balakin A.G., Smith L., and Fournier M.J. The RNA world of the nucleolus: Two major families of small nucleolar RNAs defined by different box elements with related functions. Cell 86 (1996) 823-834
2. Bachellerie J.P., Cavaille J., and Qu L.H. Nucleotide modifications of eukaryotic rRNAs: The world of small nucleolar RNA guides revisited. In: Garrett R.A., Douthwaite S., Liljas A., Matheson A., Moore P.B., and Noller H. (Eds). The Ribosome: Structure, Function, Antibiotics and Cellular Interactions (2000), ASM Press, Washington, DC 191-203
3. Darzacq X., Jady B.E., Verheggen C., Kiss A.M., Bertrand E., and Kiss T. Cajal body-specific small nuclear RNAs: A novel class of 2′-O-methylation and pseudouridylation guide RNAs. EMBO J. 21 (2002) 2746-2756
4. Huang Z.P., Zhou H., and Qu L.H. Maintaining a conserved methylation in plant and insect U2 snRNA through compensatory mutation by nucleotide insertion. IUBMB Life 57 (2005) 693-699
5. Clouet d'Orval B., Bortolin M.L., Gaspin C., and Bachellerie M.L. X 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 (2001) 4518-4529
6. Huttenhofer A., Kiefmann M., Meier-Ewert S., O'Brien J., Lehrach H., Bachellerie J.P., and Brosius J. RNomics: An experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO J. 20 (2001) 2943-2953
7. Huttenhofer A., Cavaille J., and Bachellerie J.P. Experimental RNomics: A global approach to identifying small nuclear RNAs and their targets in different model organisms. Methods Mol. Biol. 265 (2004) 409-428
8. Gu A.D., Zhou H., Yu C.H., and Qu L.H. A novel experimental approach for systematic identification of box H/ACA snoRNAs from eukaryotes. Nucleic Acids Res. 33 (2005) 1-6 e194
9. Lowe T.M., and Eddy S.R. A computational screen for methylation guide snoRNAs in yeast. Science 283 (1999) 1168-1171
10. Schattner P., Decatur W.A., Davis C.A., Ares Jr. M., Fournier M.J., and Lowe T.M. Genome-wide searching for pseudouridylation guide snoRNAs: Analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Res. 32 (2004) 4281-4296
11. Edvardsson S., Gardner P.P., Poole A.M., Hendy M.D., Penny D., and Moulton V. A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics 19 (2003) 865-873
12. Accardo M.C., Giordano E., Riccardo S., Digilio F.A., Iazzetti G., Calogero R.A., and Furia M. A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome. Bioinformatics 20 (2004) 3293-3301
13. Huang Z.P., Zhou H., Liang D., and Qu L.H. Different expression strategy: Multiple intronic gene clusters of box H/ACA snoRNA in Drosophila melanogaster. J. Mol. Biol. 341 (2004) 669-683
14. 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
15. Liang X.H., Uliel S., Hury A., Barth S., Doniger T., Unger R., and Michaeli S. A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA modification. RNA 11 (2005) 619-645
16. Tycowski K.T., You Z.H., Graham P.J., and Steitz J.A. Modification of U6 spliceosomal RNA is guided by other small RNAs. Mol. Cell 2 (1998) 629-638
17. Higa S., Maeda N., Kenmochi N., and Tanaka T. Location of 2(′)-O-methyl nucleotides in 26S rRNA and methylation guide snoRNAs in Caenorhabditis elegans. Biochem Biophys Res Commun. 297 (2002) 1344-1349
18. Wachi M., Ogawa T., Yokoyama K., Hokii Y., Shimoyama M., Muto A., and Ushida C. Isolation of eight novel Caenorhabditis elegans small RNAs. Gene 335 (2004) 47-56
19. Mitrovich Q.M., and Anderson P. mRNA surveillance of expressed pseudogenes in C. elegans. Curr. Biol. 15 (2005) 963-967
20. Deng W., Zhu X., Skogerbo G., Zhao Y., Fu Z., Wang Y., He H., Cai L., Sun H., Liu C., Li B., Bai B., Wang J., Jia D., Sun S., He H., Cui Y., Wang Y., Bu D., and Chen R. Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression. Genome Res. 16 (2006) 20-29
21. Nakao A., Yoshihama M., and Kenmochi N. RPG: The Ribosomal Protein Gene database. Nucleic Acids Res. 32 (2004) D168-D170
22. Hirose T., and Steitz J.A. Position within the host intron is critical for efficient processing of box C/D snoRNAs in mammalian cells. Proc. Natl. Acad. Sci. USA 98 (2001) 12914-12919
23. Kiss A.M., Jady B.E., Bertrand E., and Kiss T. Human box H/ACA pseudouridylation guide RNA machinery. Mol. Cell Biol. 24 (2004) 5797-5807
24. Schattner P., Barberan-Soler S., and Lowe T.M. A computational screen for mammalian pseudouridylation guide H/ACA RNAs. RNA 12 (2006) 15-25
25. Yuan G., Klambt C., Bachellerie J.P., Brosius J., and Huttenhofer A. RNomics in Drosophila melanogaster: Identification of 66 candidates for novel non-messenger RNAs. Nucleic Acids Res. 31 (2003) 2495-2507
26. Accardo M.C., Giordano E., Riccardo S., Digilio F.A., Iazzetti G., Calogero R.A., and Furia M. A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome. Bioinformatics 20 (2004) 3293-3301
27. Torchet C., Badis G., Devaux F., Costanzo G., Werner M., and Jacquier A. The complete set of H/ACA snoRNAs that guide rRNA pseudouridylations in Saccharomyces cerevisiae. RNA 11 (2005) 928-938
28. Dermitzakis E.T., Reymond A., Lyle R., Scamuffa N., Ucla C., Deutsch S., Stevenson B.J., Flegel V., Bucher P., Jongeneel C.V., and Antonarakis S.E. Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature 420 (2002) 578-582
29. Berezikov E., Guryev V., van de Belt J., Wienholds E., Plasterk R.H., and Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120 (2005) 21-24
30. Washietl S., Hofacker I.L., Lukasser M., Huttenhofer A., and Stadler P.F. Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat. Biotechnol. 23 (2005) 1383-1390
31. Brown J.W., Echeverria M., and Qu L.H. Plant snoRNAs: Functional evolution and new modes of gene expression. Trends Plant Sci. 8 (2003) 42-49
32. Brown J.W., Clark G.P., Leader D.J., Simpson C.G., and Lowe T. Multiple snoRNA gene clusters from Arabidopsis. RNA 7 (2001) 1817-1832
33. Qu L.H., Meng Q., Zhou H., and Chen Y.Q. Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana. Nucleic Acids Res. 29 (2001) 1623-1630
34. Russell A.G., Schnare M.N., and Gray M.W. Pseudouridine-guide RNAs and other Cbf5p-associated RNAs in Euglena gracilis. RNA 10 (2004) 1034-1046
35. Tycowski K.T., Alar A., and Steitz J.A. Guide RNAs with 5′ caps and novel box C/D snoRNA-like domains for modification of snRNAs in metazoa. Curr. Biol. 14 (2004) 1985-1995
36. Tycowski K.T., Shu M.D., and Steitz J.A. A mammalian gene with introns instead of exons generating stable RNA products. Nature 379 (1996) 464-466
37. Hirose T., Shu M.D., and Steitz J.A. Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells. Mol. Cell 12 (2003) 113-123
38. Valcarcel J., Gaur R.K., Singh R., and Green M.R. Interaction of U2AF65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA. Science 273 (1996) 1706-1709
39. Blumenthal T., and Steward K. In: Riddle D., Blumenthal T., Meyer B., and Priess J. (Eds). C. elegans II (1997), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY 117-145
40. Zorio D.A., and Blumenthal T. Both subunits of U2AF recognize the 3′ splice site in Caenorhabditis elegans. Nature 402 (1999) 835-838
41. Brudno M., Do C.B., Cooper G.M., Kim M.F., Davydov E., Green E.D., Sidow A., and Batzoglou S. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13 (2003) 721-731
42. Mayor C., Brudno M., Schwartz J.R., Poliakov A., Rubin E.M., Frazer K.A., Pachter L.S., and Dubchak I. VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16 (2000) 1046-1047
43. Chomczynski P., and Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162 (1987) 732-735
44. Zhou H., Chen Y.Q., Du Y.P., and Qu L.H. The Schizosaccharomyces pombe mgU6-47 gene is required for 2′-O-methylation of U6 snRNA at A41. Nucleic Acids Res. 30 (2002) 894-902
45. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual. 2nd ed. (1989), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY