The RNA world of the nucleolus: Two major families of small RNAs defined by different box elements with related functions

Cell

Volumn 86, Issue 5, 1996, Pages 823-834

  Balakin, Andrey G ^a   Smith, Laurie ^a   Fournier, Maurille J ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; HYDROLYSIS; INTRON; METHYLATION; NONHUMAN; NUCLEOLUS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FAMILY; PROTEIN STABILITY; RIBOSOME SUBUNIT; RNA SYNTHESIS; RNA TRANSCRIPTION; TATA BOX;

EID: 0030572699     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)80156-7     Document Type: Article

References (47)

1. Aris, J.P., and Blobel, G. (1991). Isolation of yeast nuclei. Meth. Enzymol. 194, 735-749.
2. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K., eds. (1994). Current Protocols in Molecular Biology (New York: John Wiley and Sons).
3. Balakin, A.G., Schneider, G.S., Corbett, M.S., Ni, J., and Fournier, M. J. (1993). snR31, snR32, snR33, three novel nonessential snRNAs from Saccharomyces cerevisiae. Nucl. Acids Res. 21, 5391-97.
4. Balakin, A.G., Lempicki, R.A., Huang, G.M., and Fournier, M.J. (1994). Saccharomyces cerevisiae U14 small nuclear RNA has little secondary structure and appears to be produced by posttranscriptional processing. J. Biol. Chem. 269, 739-746.
5. Caffarelli, E., Fatica, A., Prisley, S., De Gregorio, E., Fragapane, P., and Bozzoni, I. (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. 5, 1121-1131.
6. XS8, a small nucleolar RNA with a 12 nt complementarity to 18S rRNA and coded by a sequence repeated in the six introns of Xenopus laevis ribosomal protein S8 gene. Nucl. Acids Res. 22, 732-741.
7. Chen, B., and Przybyla, A.E. (1994). An efficient site-directed mutagenesis method based on PCR. Biotechniques 17, 657-659.
8. Chu, S., Archer, R.H., Zengel, J.M., and Lindahl, L. (1994). The RNA of RNase MRP is required for normal processing of ribosomal RNA. Proc. Natl. Acad. Sci. USA 91, 659-663.
9. Clark, M.W., Yip, M.L.R., Campbell, J., and Abelson, J. (1991). SSB-1 of the yeast Saccharomyces cerevisiae is a nucleolar-specific silver-binding protein that is associated with the snR10 and snR11 small nuclear RNAs. J. Cell Biol. 111, 1741-1751.
10. Dandekar, T., and Tollervey, D. (1993). Identification and functional analysis of a novel yeast small nucleolar RNA. Nucl. Acids Res. 21, 5386-5390.
11. Eichler, D., and Craig, N. (1994). Processing of eukaryotic ribosomal RNA. Prog. Nucl. Acids Res. Mol. Biol. 49, 197-239.
12. Forster, A.C., and Altman, S. (1991). Similar cage-shaped structure for the RNA components of all ribonuclease P and ribonuclease MRP enzymes. Cell 62, 407-409.
13. Gietz, D., Jean, A.S., Woods, R.A., and Schiestl, R.H. (1992). Improved method for high efficiency transformation of intact yeast cells. Nucl. Acids Res. 20, 1425.
14. Girard, J.P., Lehtonen, H., Caizergues-Ferrer, M., Amalric, F., Tollervey, D, and Lapeyre, B. (1992). GAR1 is an essential small nucleolar RNP protein required for pre-rRNA processing in yeast Saccharomyces cerevisiae. EMBO J. 11, 673-682.
15. Gold, H.A., Craft, J., Hardin, J.A., Bartkiewicz, M., and Altman, S. (1988). Antibodies in human serum that precipitate ribonuclease P. Proc. Natl. Acad. Sci. USA 85, 5483-5487.
16. Harlow, E., and Lane, D., eds. (1988). Antibodies (Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press).
17. Huang, G.M., Jarmolowski, A., Struck, J.C.R., and Fournier, M.J. (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.
18. Kiss, T., and Filipowicz, W. (1993). Small nucleolar RNAs encoded by introns of the human cell cycle regulatory gene RCC1. EMBO J. 12, 2913-2920.
19. Kiss, T., Bortlin, M.-L., and Filipowicz, W. (1996). Characterization of the intron-encoded U19 RNA, a new mammalian small nucleolar RNA that is not associated with fibrillarin. Mol. Cell. Biol. 16, 1391-1400.
20. Kiss-László, 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.
21. Leverette, R.D., Andrews, M.T., and Maxwell, E.S. (1992). Mouse U14 snRNA is a processed intron of the cognate hsc70 heat shock pre-messenger RNA. Cell 71, 1215-1221.
22. Lübben, B., Marshallsay, C., Rottmann, N., and Lührmann, R. (1993). Isolation of U3 snoRNA from CHO cells: a novel 55 kDa protein binds to the central part of U3 snoRNA. Nucl. Acids Res. 21, 5377-5385.
23. Lübben, B., Fabrizio, P., Kastner, B., and Lührmann, R. (1995). Isolation and characterization of the small nucleolar ribonucleoprotein particle snR30 from Saccharomyces cerevisiae. J. Biol. Chem. 27O, 11549-11554.
24. Lygerou, Z., Mitchell, P., Petfalski, E., Seraphin, B., and Tollervey, D. (1994). The POP1 gene encodes a protein component common to the RNase MRP and RNase P ribonucleoproteins. Genes Dev. 8, 1423-1433.
25. Lygerou, Z., Allmang, C., Tollervey, D., and Séraphin, B. (1996). Accurate processing of a eukaryotic precursor ribosomal RNA by ribonuclease MRP in vitro. Science 272, 268-270.
26. Maxwell, E.S., and Fournier, M.J. (1995). The nucleolar small RNAs. Annu. Rev. Biochem. 35, 897-934.
27. Nicoloso, M., Qu, L.-H., Michot, B., and Bachellerie, J.-P. (1996). Intron-encoded antisense small nucleolar RNAs: the characterization of nine novel species points to their role as guides for the 2'-O-ribose methylation of rRNAs. J. Mol. Biol., 260, 178-195.
28. Ochman, H., Ajioka, J.W., Garza, D., and Hartl, D.L. (1989). Inverse polymerase chain reaction. In PCR Technology, H.A. Erlich, ed. (New York: Stockton Press), pp. 105-111.
29. Parker, R., Simmons, T., Shuster, E.O., Siliciano, P.G., and Guthrie, C. (1988). Genetic analysis of small nuclear RNAs in Saccharomyces cerevisiae: a viable sextuple mutant. Mol. Cell. Biol. 8, 3150-3159.
30. Peattie, D.A. (1979). Direct chemical method for sequencing RNA. Proc. Natl. Acad. Sci. USA 76, 1760-1764.
31. Peculis, B.A., and Steitz, J.A. (1994). Sequence and structural elements critical for U8 snRNP function in Xenopus oocytes are evolutionarily conserved. Genes Dev. 8, 2241-2255.
32. Qu, L.-H., Henry, Y., Nicoloso, M., Michot, B., Azum, M.-C., Renalier, M., Caizergues-Ferrer, M., and Bachellerie, J.-P. (1995). U24, a novel intron-encoded small nucleolar RNA with two 12 nt long phylogenetically conserved complementarities to 28S rRNA. Nucl. Acids Res. 23, 2669-2676.
33. Riedel, N., Wise, J.A., Swerdlow, H., Mak, A., and Guthrie, C. (1986). Small nuclear RNAs for S. cerevisiae: unexpected diversity in abundance, size, and molecular complexity. Proc. Natl. Acad. Sci. USA 83, 8097-8101.
34. Ruff, E.A., Rimoldi, O.J., Raghu, B., and Eliceiri, G.L. (1993). Three small nucleolar RNAs of unique nucleotide sequences. Proc. Natl. Acad. Sci. USA 90, 635-638.
35. Samarsky, D., Balakin, A.G., and Fournier, M.J. (1995). Characterization of three new snRNAs from Saccharomyces cerevisiae: snR34, snR35, and snR36. Nucl. Acids Res. 23, 2548-2554.
36. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989). Molecular Cloning, Second Edition (Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press).
37. Schimmang, T., Tollervey, D., Kern, H., Frank, R., and Hurt, E.C. (1989). A yeast nucleolar protein related to mammalian fibrillarin is associated with small nucleolar RNA and is essential for viability. EMBO J. 8, 4015-4024.
38. Schmitt, M.E., and Clayton, D.A. (1993). Nuclear RNase MRP is required for correct processing of pre-5.8S rRNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 13, 7935-7941.
39. Schmitt, M.E., Bennet, J.L., Dairaghi, D.J., and Clayton, D.A. (1993). Secondary structure of RNase MRP RNA as predicted by phylogenetic comparison. FASEB J. 7, 208-213.
40. Terns, M.P., Grimm, C., Lund, L., and Dahlberg, J.E. (1995). A common maturation pathway for small nucleolar RNAs. EMBO J. 14, 4860-4871.
41. Tycowski, K.T., Shu, M.D., and Steitz, J.A. (1993). A small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein S13. Genes Dev. 7, 1176-1190.
42. Tycowski, K.T., Shu, M.D., and Steitz, J.A. (1996). A mammalian gene with introns instead of exons generating stable RNA products. Nature 379, 464-466.
43. Venema, J., and Tollervey, D. (1995). Processing of pre-ribosomal RNA in Saccharomyces cerevisiae. Yeast 11, 1629-1650.
44. Watkins, N.J., Leverette, R.D., Xia, L., Andrews, M.T., and Maxwell, E.S. (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.
45. Wise, J.A. (1991). Preparation and analysis of low molecular weight RNAs and small ribonucleoproteins. Meth. Enzymol. 194, 405-415.
46. Wise, J.A., Tollervey, D., Maloney, D., Swerdlow, H., Dunn, E.J., and Guthrie, C. (1983). Yeast contains small nuclear RNAs encoded by single-copy genes. Cell 35, 743-751.
47. Zubenko, G.S., Mitchell, A.P., and Jones, E.W. (1980). Mapping of the proteinase b structural gene PRB1 in Saccharomyces cerevisiae and identification of nonsense alleles within the locus. Genetics 96, 137-146.