Functional mapping of the U3 small nucleolar RNA from the yeast Saccharomyces cerevisiae

Molecular and Cellular Biology

Volumn 18, Issue 6, 1998, Pages 3431-3444

  Samarsky, Dmitry A ^a   Fournier, Maurille J ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GALACTOSE; GLUCOSE; RIBOSOME RNA; RNA 18S; SMALL NUCLEOLAR RNA; TRANS ACTING FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; GENE MAPPING; GENETIC CONSERVATION; NONHUMAN; NORTHERN BLOTTING; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RNA STRUCTURE; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 0031816004     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.18.6.3431     Document Type: Article

References (79)

1. Ares, M., Jr. 1986. U2 RNA from yeast is unexpectedly large and contains homology to vertebrate U4, U5, and U6 small nuclear RNAs. Cell 47:49-59.
2. Bachellerie, J. P., and J. Cavaille. 1997. Guiding rihose methylation of rRNA. Trends Biochem. Sci. 22:257-261.
3. Balakin, A. G., R. A. Lempicki, G. M. Huang, and M. J. Fournier. 1994. Saccharomyces cerevisiae U14 small nuclear RNA has little secondary structure and appears to be produced by post-transcriptional processing. J. Biol. Chem. 269:739-746.
4. Balakin, A. G., G. S. Schneider, M. S. Corbett, J. Ni, and M. J. Fournier. 1993. SnR31, snR32, and snR33: three novel, non-essential snRNAs from Saccharomyces cerevisiae. Nucleic Acids Res. 21:5391-5397.
5. Baserga, S. J., M. Gilmore-Hebert, and X. W. Yang. 1992. Distinct molecular signals for nuclear import of the nucleolar snRNA, U3. Genes Dev. 6:1120-1130.
6. Baserga, S. J., X. W. Yang, and J. A. Steitz. 1991. An intact box C sequence in the U3 snRNA is required for binding of fibrillarin, the protein common to the major family of nucleolar snRNPs. EMBO J. 10:2645-2651.
7. Beltrame, M., Y. Henry, and D. Tollervey. 1994. Mutational analysis of an essential binding site for the U3 snoRNA in the 5′ external transcribed spacer of yeast pre-rRNA. Nucleic Acids Res. 22:5139-5147.
8. Beltrame, M., and D. Tollervey. 1995. Base pairing between U3 and the pre-ribosomal RNA is required for 18S rRNA synthesis. EMBO J. 14:4350-4356.
9. Beltrame, M., and D. Tollervey. 1992. Identification and functional analysis of two U3 binding sites on yeast pre-ribosomal RNA. EMBO J. 11:1531-1542.
10. Bernstein, L. B., S. M. Mount, and A. M. Weiner. 1983. Pseudogenes for human small nuclear RNA U3 appear to arise by integration of self-primed reverse transcripts of the RNA into new chromosomal sites. Cell 32:461-472.
11. Brule, F., J. Venema, V. Segault, D. Tollervey, and C. Branlant. 1996. The yeast Hansenula wingei U3 snoRNA gene contains an intron and its coding sequence co-evolved with the 5′ ETS of the pre-ribosomal RNA. RNA 2:183-197.
12. Caffarelli, E., A. Fatica, S. Prislei, E. De Gregorio, P. Fragapane, and I. Bozzoni. 1996. Processing of the intron-encoded U16 and U18 snoRNAs: the conserved C and D boxes control both the processing reaction and the stability of the mature snoRNA. EMBO J. 15:1121-1131.
13. Cavaille, J., and J. P. Bachellerie. 1996. Processing of fibrillarin-associated snoRNAs from pre-mRNA introns: an exonucleolytic process exclusively directed by the common stem-box terminal structure. Biochimie 78:443-456.
14. Cavaille, J., M. Nicoloso, and J.-P. Bachellerie, 1996. Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature 383:732-735.
15. Dunbar, D. A., S. Wormsley, T. M. Agentis, and S. J. Baserga. 1997. Mpp10p, a U3 small nucleolar ribonucleoprotein component required for pre-18S rRNA processing in yeast. Mol. Cell. Biol. 17:5803-5812.
16. Fournier, M. J., and E. S. Maxwell. 1993. The nucleolar snRNAs: catching up with the spliceosomal snRNAs. Trends Biochem. Sci. 18:131-135.
17. Gerbi, S. A. 1995. Small nucleolar RNA. Biochem. Cell Biol. 73:845-858.
18. Greenwood, S. J., M. N. Schnare, and M. W. Gray. 1996. Molecular characterization of U3 small nucleolar RNA from the early diverging protist, Euglena gracilis. Curr. Genet. 30:338-346.
19. Gu, J., and R. Reddy. 1997. Small RNA database. Nucleic Acids Res. 25:98-102.
20. Hanahan, D., J. Jessee, and F. R. Bloom. 1991. Plasmid transformation of Escherichia coli and other bacteria. Methods Enzymol. 204:63-113.
21. Hartshorne, T., and N. Agabian. 1994. A common core structure for U3 small nucleolar RNAs. Nucleic Acids Res. 22:3354-3364.
22. Hartshorne, T., and N. Agabian. 1993. RNA B is the major nucleolar trimethylguanosine-capped small nuclear RNA associated with fibrillarin and pre-rRNAs in Trypanosoma brucei. Mol. Cell. Biol. 13:144-154.
23. Huang, G. M., A. Jarmolowski, J. C. R. Struck, and M. J. Fournier. 1992. Accumulation of U14 small nuclear RNA in Saccharomyces cerevisiae requires box C, box D, and a 5′, 3′ terminal stem. Mol. Cell. Biol. 12:4456-4463.
24. Hughes, J. M. X. 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.
25. Hughes, J. M. X., and M. Ares, Jr. 1991. Depletion of U3 small nucleolar RNA inhibits cleavage in the 5′ external transcribed spacer of yeast pre-ribosomal RNA and impairs formation of 18S ribosomal RNA. EMBO J. 10:4231-4239.
26. Hughes, J. M. X., D. A. M. Konings, and G. Cesareni. 1987. The yeast homologue of U3 snRNA. EMBO J. 6:2145-2155.
27. Jansen, R., D. Tollervey, and E. C. Hurt. 1993. A U3 snoRNP protein with homology to splicing factor PRP4 and Gβ domains is required for ribosomal RNA processing. EMBO J. 12:2549-2558.
28. Jeppesen, C., B. Stebbins-Boaz, and S. A. Gerbi. 1988. Nucleotide sequence determination and secondary structure of Xenopns U3 snRNA. Nucleic Acids Res. 16:2127-2148.
29. Kass, S., K. Tyc, J. A. Steitz, and B. Sollner-Webb. 1990. The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing. Cell 60:897-908.
30. Kiss, T., and F. Solymosy. 1990. Molecular analysis of a U3 RNA gene locus in tomato: transcription signals, the coding region, expression in transgenic tobacco plants and tandemly repeated pseudogenes. Nucleic Acids Res. 18:1941-1949.
31. Kiss, T., M. Toth, and F. Solymosy. 1985. Plant small nuclear RNAs. Nucleolar U3 snRNA is present in plants: partial characterization. Eur. J. Biochem. 152:259-266.
32. Kiss-Laszlo, Z., Y. Henry, J. P. Bachellerie, M. Caizergues-Ferrer, and T. Kiss. 1996. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85:1077-1088.
33. Kohrer, K., and H. Domdey. 1991. Preparation of high molecular weight RNA. Methods Enzymol. 194:398-405.
34. Leader, D. J., S. Connelly, W. Filipowicz, and J. W. S. Brown. 1994. Characterization and expression of a maize U3 snRNA gene. Biochim. Biophys. Acta 1219:145-147.
35. Lempicki, R. A., and M. J. Fournier. 1994. Unpublished data.
36. Li, H. V., and M. J. Fournier. 1992. U14 function in Saccharomyces cerevisiae can be provided by large deletion variants of yeast U14 and hybrid mouse-yeast U14 RNAs. EMBO J. 11:683-689.
37. Lubben, B., C. Marshallsay, N. Rottmann, and R. Luhrmann. 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.
38. Maden, T. 1996. Click here for methylation. Nature 383:675-676.
39. Marshallsay, C., S. Connelly, and W. Filipowicz. 1992. Characterization of the U3 and U6 snRNA genes from wheat: U3 snRNA genes in monocot plants are transcribed by RNA polymerase III. Plant Mol. Biol. 19:973-983.
40. Maxwell, E. S., and M. J. Fournier. 1995. The small nucleolar RNAs. Annu. Rev. Biochem. 35:897-934.
41. Mazan, S., and J. P. Bachellerie. 1988. Structure and organization of mouse U3B RNA functional genes. J. Biol. Chem. 263:19461-19467.
42. Mazan, S., M. P. Gulli, N. Joseph, and J. P. Bachellerie. 1992. Structure of the differentially expressed mouse U3A gene. Eur. J. Biochem. 205:1033-1041.
43. Mazan, S., L. H. Qu, J. Sri-Widada, M. Nicoloso, and J. P. Bachellerie. 1990. Presence of a differentially expressed U3A RNA variant in mouse. Structure and evolutive implications. FEBS Lett. 267:121-125.
44. Mereau, A., R. Fournier, A. Gregoire, A. Mougin, P. Fabrizio, R. Luhrmann, and C. Branlant. 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. 273:552-571.
45. Mougey, E. B., L. K. Pape, and B. Sollner-Webb. 1993. A U3 small nuclear ribonucleoprotein-requiring processing event in the 5′ external transcribed spacer of Xenopus precursor rRNA. Mol. Cell. Biol. 13:5990-5998.
46. Mougin, A., A. Gregoire, J. Banroques, V. Segault, R. Fournier, F. Brule, M. Chevrier-Miller, and C. Branlant. 1996. Secondary structure of the yeast Saccharomyces cerevisiae pre-U3A snoRNA and its implication for splicing efficiency. RNA 2:1079-1093.
47. Myslinski, E., V. Segault, and C. Branlant. 1990. An intron in the genes for U3 small nucleolar RNAs of the yeast Saccharomyces cerevisiae. Science 247:1213-1216.
48. Nicoloso, M., L. H. Qu, B. Michot, and J. P. Bachellerie. 1996. Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2′-O-ribose methylation of rRNAs. J. Mol. Biol. 260:178-195.
49. Orum, H., H. Nielsen, and J. Engberg. 1993. Sequence and proposed secondary structure of the Tetrahymena thermophila U3-snRNA. Nucleic Acids Res. 21:2511.
50. Parker, K. A., and J. A. Steitz. 1987. Structural analyses of the human U3 ribonucleoprotein particle reveal a conserved sequence available for base pairing with pre-rRNA. Mol. Cell. Biol. 7:2899-2913.
51. Peculis, B. A., and S. M. Mount. 1996. Ribosomal RNA: small nucleolar RNAs make their mark. Curr. Opin. Cell Biol. 6:1413-1415.
52. Porter, G. L., P. J. Brennwald, K. A. Holm, and J. A. Wise. 1988. The sequence of U3 from Schizosaccharomyces pombe suggests structural divergence of this snRNA between metazoans and unicellular eukaryotes. Nucleic Acids Res. 16:10131-10152.
53. Reddy, R., D. Henning, and H. Busch. 1979. Nucleotide sequence of nucleolar U3B RNA. J. Biol. Chem. 254:11097-11105.
54. Rose, M. D., F. Winston, and P. Heiter. 1990. Methods in yeast genetics: a laboratory course manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
55. Samarsky, D. A., A. G. Balakin, and M. J. Fournier. 1995. Characterization of three new snRNAs from Saccharomyces cerevisiae: snR34, snR35, and snR36. Nucleic Acids Res. 23:2548-2554.
56. Samarsky, D. A., E. Bertrand, R. H. Singer, and M. J. Fournier. Unpublished data.
57. Samarsky, D. A., G. Ferbeyre, E. Bertrand, R. H. Singer, R. Cedergren, and M. J. Fournier. Unpublished data.
58. Samarsky, D. A., and M. J. Fournier. 1996. Unpublished data.
59. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
60. Savino, R., and S. A. Gerbi. 1990. In vivo disruption of Xenopus U3 snRNA affects ribosomal RNA processing. EMBO J. 9:2299-2308.
61. Segault, V., A. Mougin, A. Gregoire, J. Banroques, and C. Branlant. 1992. An experimental study of Saccharomyces cerevisiae U3 snRNA conformation in solution. Nucleic Acids Res. 20:3443-3451.
62. Selinger, D. A., G. L. Porter, P. J. Brennwald, and J. A. Wise. 1992. The two similarly expressed genes encoding U3 snRNA in Schizosaccharomyces pombe lack introns. Mol. Biol. Evol. 9:297-308.
63. Shuster, E. O., and C. Guthrie. 1988. Two conserved domains of yeast U2 snRNA are separated by 945 nonessential nucleotides. Cell 55:41-48.
64. Sikorski, R. S., and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19-27.
65. Smith, C. M., and J. A. Steitz. 1997. Sno storm in the nucleolus: new roles for myriad small RNPs. Cell 89:669-672.
66. Stroke, I. L., and A. M. Weiner. 1989. The 5′ end of U3 snRNA can be crosslinked in vivo to the external transcribed spacer of rat ribosomal RNA precursor. J. Mol. Biol. 210:497-512.
67. Terns, M. P., and J. E. Dahlberg. 1994. Retention and 5′ cap trimethylation of U3 snRNA in the nucleus. Science 264:959-961.
68. Terns, M. P., C. Grimm, E. Lund, and J. Dahlberg. 1995. A common maturation pathway for small nucleolar RNAs. EMBO J. 14:4860-4871.
69. Tollervey, D., and T. Kiss. 1997. Function and synthesis of small nucleolar RNAs. Curr. Opin. Cell Biol. 9:337-342.
70. Tollervey, D., H. Lehtonen, M. Carmo-Fonseca, and E. C. Hurt. 1991. The small nucleolar RNP protein NOP1 (fibrillarin) is required for pre-rRNA processing in yeast. EMBO J. 10:573-583.
71. Tollervey, D., H. Lehtonen, R. Jansen, H. Kern, and E. C. Hurt. 1993. Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly. Cell 72:443-457.
72. Tyc, K., and J. A. Steitz. 1992. A new interaction between the mouse 5′ external transcribed spacer of pre-rRNA and the U3 snRNA detected by psoralen crosslinking. Nucleic Acids Res. 20:5375-5382.
73. Tyc, K., and J. A. Steitz. 1989. U3, U8 and U13 comprise a new class of mammalian snRNPs localized in the cell nucleolus. EMBO J. 8:3113-3119.
74. Tycowski, K. T., M. D. Shu, and J. A. Steitz. 1993. A small nucleolar RNA is processed from an intron of the human gene encoding rihosomal protein S3. Genes Dev. 7:1176-1190.
75. Tycowski, K. T., C. M. Smith, M. D. Shu, and J. A. Steitz. 1996. A small nucleolar RNA requirement for site-specific rihose mcthylation of rRNA in Xenopus. Proc. Natl. Acad. Sci. USA 93:14480-14485.
76. Watkins, N. J., R. D. Leverette, L. Xia, M. T. Andrews, and E. S. Maxwell. 1996. Elements essential for processing intronic U14 snoRNA are located at the termini of the mature snoRNA sequence and include conserved nucleotide boxes C and D. RNA 2:118-133.
77. Wise, J. A., and A. M. Weiner. 1980. Dictyostelium small nuclear RNA D2 is homologous to rat nucleolar RNA U3 and is encoded by a dispersed multigene family. Cell 22:109-118.
78. Xia, L., N. J. Watkins, and E. S. Maxwell. 1997. Identification of specific nucleotide sequences and structural elements required for intronic U14 snoRNA processing. RNA 3:17-26.
79. Zwieb, C. 1996. The uRNA database. Nucleic Acids Res. 24:76-79.