Skip to main content

Mechanisms and functions of RNA-guided RNA modification

  • Chapter
  • First Online:
Fine-Tuning of RNA Functions by Modification and Editing

Part of the book series: Topics in Current Genetics ((TCG,volume 12))

Abstract

RNA-guided 2’-O-methylations and pseudouridylations occur in several different types of RNAs and in a wide range of organisms. Hundreds of the RNAs that guide these modifications have been identified, leading to breakthroughs in our understanding of the mechanisms of RNA-guided RNA modifications and, to some extent, the functions of 2’-O-methylated residues and pseudouridines. There are two classes of guide RNAs, namely box C/D and box H/ACA RNAs, which direct 2’-O-methylations and pseudouridylations, respectively. The guide RNAs function primarily by binding to complementary regions in the target RNAs. Cel-lular guide RNAs exist in RNA-protein complexes comprised of one guide RNA and a set of proteins that includes the modifying enzyme (2’-O-methylase or pseu-douridylase). We are beginning to understand the basis for the importance of the RNA-guided modifications, which are well conserved and clustered in function-ally important regions of RNAs. Recent reports indicate that modified nucleotides in rRNAs and spliceosomal snRNAs contribute to protein synthesis and pre-mRNA splicing, respectively.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • 1. Accardo MC, Giordano E, Riccardo S, Digilio FA, Iazzetti G, Calogero RA, Furia M (2004) A computational search for box C/D snoRNA genes in the D. melanogaster ge-nome. Bioinformatics, Advance Access published online on August 5, 2004

    Google Scholar 

  • 2. Aittaleb M, Rashid R, Chen Q, Palmer JR, Daniels CJ, Li H (2003) Structure and function of archaeal box C/D sRNP core proteins. Nat Struct Biol 10:256-263

    Google Scholar 

  • 3. Alexandrov A, Martzen MR, Phizicky EM (2002) Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA 8:1253-1266

    Article  Google Scholar 

  • 4. Arnez JG, Steitz TA (1994) Crystal structure of unmodified tRNA(Gln) complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure. Biochemistry 33:7560-7567

    Google Scholar 

  • 5. Auffinger P, Westhof E (1998) Location and distribution of modified nucleotides in tRNA. In: Grosjean H, Benne R (eds) Modification and Editing of RNA. ASM Press, Wash-ington, DC, pp 569-576

    Google Scholar 

  • 6. Bachellerie J-P, Cavaille J (1998) Small nucleolar RNAs guide the ribose methylations of eukaryotic rRNAs. In: Grosjean H, Benne R (eds) Modification and Editing of RNA. ASM Press, Washington, DC, pp 255-272

    Google Scholar 

  • 7. Bachellerie JP, Cavaille J (1997) Guiding ribose methylation of rRNA. Trends Biochem Sci 22:257-261

    Google Scholar 

  • 8. Bachellerie JP, Cavaille J, Huttenhofer A (2002) The expanding snoRNA world. Biochimie 84:775-790

    Article  CAS  PubMed  Google Scholar 

  • 9. Bachellerie JP, Michot B, Nicoloso M, Balakin A, Ni J, Fournier MJ (1995) Antisense snoRNAs: a family of nucleolar RNAs with long complementarities to rRNA. Trends Biochem Sci 20:261-264

    Article  Google Scholar 

  • 10. Badis G, Fromont-Racine M, Jacquier A (2003) A snoRNA that guides the two most con-served pseudouridine modifications within rRNA confers a growth advantage in yeast. RNA 9:771-779

    Google Scholar 

  • 11. Bagni C, Lapeyre B (1998) Gar1p binds to the small nucleolar RNAs snR10 and snR30 in vitro through a nontypical RNA binding element. J Biol Chem 273:10868-10873

    Google Scholar 

  • 12. Bakin A, Ofengand J (1993) Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the appli-cation of a new sequencing technique. Biochemistry 32:9754-9762

    Google Scholar 

  • 13. Balakin AG, Schneider GS, Corbett MS, Ni J, Fournier MJ (1993) SnR31, snR32, and snR33: three novel, non-essential snRNAs from Saccharomyces cerevisiae. Nucleic Acids Res 21:5391-5397

    Google Scholar 

  • 14. Balakin AG, Smith L, Fournier MJ (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

    Google Scholar 

  • 15. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289:905-920

    Google Scholar 

  • 16. Barneche F, Gaspin C, Guyot R, Echeverria M (2001) Identification of 66 box C/D snoR-NAs in Arabidopsis thaliana: extensive gene duplications generated multiple isoforms predicting new ribosomal RNA 2’-O-methylation sites. J Mol Biol 311:57-73

    Google Scholar 

  • 17. Bjork GR (1995) Biosynthesis and function of modified nucleotides. In: Soll D, RajBhan-dary U (eds) tRNA: Structure, biosynthesis, and function. ASM Press, Washington, DC, pp 165-205

    Google Scholar 

  • 18. Bortolin ML, Bachellerie JP, Clouet-d’Orval B (2003) In vitro RNP assembly and methyla-tion guide activity of an unusual box C/D RNA, cis-acting archaeal pre-tRNA(Trp). Nucleic Acids Res 31:6524-6535

    Google Scholar 

  • 19. Bortolin ML, Ganot P, Kiss T (1999) Elements essential for accumulation and function of small nucleolar RNAs directing site-specific pseudouridylation of ribosomal RNAs. EMBO J 18:457-469

    Google Scholar 

  • 20. Bortolin ML, Kiss T (1998) Human U19 intron-encoded snoRNA is processed from a long primary transcript that possesses little potential for protein coding. RNA 4:445-454

    Google Scholar 

  • 21. Bousquet-Antonelli C, Henry Y, G’elugne JP, Caizergues-Ferrer M, Kiss T (1997) A small nucleolar RNP protein is required for pseudouridylation of eukaryotic ribosomal RNAs. EMBO J 16:4770-4776

    Google Scholar 

  • 22. Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T (2001) Multiple snoRNA gene clusters from Arabidopsis. RNA 7:1817-1832

    Google Scholar 

  • 23. Brown JW, Echeverria M, Qu LH (2003a) Plant snoRNAs: functional evolution and new modes of gene expression. Trends Plant Sci 8:42-49

    Google Scholar 

  • 24. Brown JW, Echeverria M, Qu LH, Lowe TM, Bachellerie JP, Huttenhofer A, Kastenmayer JP, Green PJ, Shaw P, Marshall DF (2003b) Plant snoRNA database. Nucleic Acids Res 31:432-435

    Google Scholar 

  • 25. Caffarelli E, Arese M, Santoro B, Fragapane P, Bozzoni I (1994) In vitro study of process-ing of the intron-encoded U16 small nucleolar RNA in Xenopus laevis. Mol Cell Biol 14:2966-2974

    Google Scholar 

  • 26. Caffarelli E, Fatica A, Prislei S, De Gregorio E, Fragapane P, 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 15:1121-1131

    Google Scholar 

  • 27. Cahill NM, Friend K, Speckmann W, Li ZH, Terns RM, Terns MP, Steitz JA (2002) Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP. EMBO J 21:3816-3828

    Google Scholar 

  • 28. Cavaille J, Buiting K, Kiefmann M, Lalande M, Brannan CI, Horsthemke B, Bachellerie JP, Brosius J, Huttenhofer A (2000) Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc Natl Acad Sci USA 97:14311-14316

    Google Scholar 

  • 29. Cavaille J, Nicoloso M, Bachellerie JP (1996) Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature 383:732-735

    Google Scholar 

  • 30. Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH (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

    Google Scholar 

  • 31. Chen JL, Blasco MA, Greider CW (2000) Secondary structure of vertebrate telomerase RNA. Cell 100:503-514

    Google Scholar 

  • 32. Clouet d’Orval B, Bortolin ML, Gaspin C, Bachellerie JP (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

    Article  Google Scholar 

  • 33. Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, 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

    Article  Google Scholar 

  • 34. Davis DR (1995) Stabilization of RNA stacking by pseudouridine. Nucleic Acids Res 23:5020-5026

    Google Scholar 

  • 35. Davis DR (1998) Biophysical and conformational properties of modified nucleotides in RNA. In: Grosjean H, Benne R (eds) Modification and editing of RNA. ASM Press, Washington, DC, pp 85-102

    Google Scholar 

  • 36. Decatur WA, Fournier MJ (2002) rRNA modifications and ribosome function. Trends Bio-chem Sci 27:344-351

    Google Scholar 

  • 37. Decatur WA, Fournier MJ (2003) RNA-guided nucleotide modification of ribosomal and other RNAs. J Biol Chem 278:695-698

    Article  Google Scholar 

  • 38. Deng L, Starostina NG, Liu ZJ, Rose JP, Terns RM, Terns MP, Wang BC (2004) Structure determination of fibrillarin from the hyperthermophilic archaeon Pyrococcus furiosus. Biochem Biophys Res Commun 315:726-732

    Google Scholar 

  • 39. Dennis PP, Omer A, Lowe T (2001) A guided tour: small RNA function in Archaea. Mol Microbiol 40:509-519

    Google Scholar 

  • 40. Donmez G, Hartmuth K, Luhrmann R (2004) Modified nucleotides in the 5’ end of the hu-man U2 snRNA are required for early spliceosome (E complex) formation in vitro. The 2004 RNA meeting abstract:92

    Google Scholar 

  • 41. Dragon F, Pogacic V, Filipowicz W (2000) In vitro assembly of human H/ACA small nu-cleolar RNPs reveals unique features of U17 and telomerase RNAs. Mol Cell Biol 20:3037-3048

    Article  CAS  PubMed  Google Scholar 

  • 42. Dunbar DA, Wormsley S, Lowe TM, Baserga SJ (2000) Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei. Sequence conservation and implica-tions for 2’-O-ribose methylation of rRNA. J Biol Chem 275:14767-14776

    Google Scholar 

  • 43. Ferre-D’Amare AR (2003) RNA-modifying enzymes. Curr Opin Struct Biol 13:49-55

    Google Scholar 

  • 44. Filipowicz W (2000) Imprinted expression of small nucleolar RNAs in brain: time for RNomics. Proc Natl Acad Sci USA 97:14035-14037

    Google Scholar 

  • 45. Filipowicz W, Pogacic V (2002) Biogenesis of small nucleolar ribonucleoproteins. Curr Opin Cell Biol 14:319-327

    Article  CAS  PubMed  Google Scholar 

  • 46. Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I (2002) Purified box C/D snoRNPs are able to reproduce site-specific 2’-O-methylation of target RNA in vitro. Mol Cell Biol 22:6663-6668

    Google Scholar 

  • 47. Ganot P, Bortolin ML, Kiss T (1997a) Site-specific pseudouridine formation in preribo-somal RNA is guided by small nucleolar RNAs. Cell 89:799-809

    Google Scholar 

  • 48. Ganot P, Caizergues-Ferrer M, Kiss T (1997b) The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes Dev 11:941-956

    Google Scholar 

  • 49. Ganot P, Jady BE, Bortolin ML, Darzacq X, Kiss T (1999) Nucleolar factors direct the 2’-O-ribose methylation and pseudouridylation of U6 spliceosomal RNA. Mol Cell Biol 19:6906-6917

    Google Scholar 

  • 50. Gaspin C, Cavaille J, Erauso G, Bachellerie JP (2000) Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. J Mol Biol 297:895-906

    Google Scholar 

  • 51. Gautier T, Berges T, Tollervey D, Hurt E (1997) Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis. Mol Cell Biol 17:7088-7098

    Google Scholar 

  • 52. Gerbi SA, Savino R, Stebbins-Boaz B, Jeppesen C, Rivera-Leon R (1990) A role for U3 small nuclear ribonucleoprotein in the nucleolus? In: Dahlberg A, Garrett RA, Moore PB, Schlessinger D, Warner JR (eds) The ribosome-structure, function and evolution. ASM Press, Washington, DC, pp 452-469

    Google Scholar 

  • 53. Grosjean H, Keith G, Droogmans L (2004) Detection and quantification of modified nu-cleotides in RNA using thin-layer chromatography. Methods Mol Biol 265:357-391

    Google Scholar 

  • 54. Grosjean H, Sprinzl M, Steinberg S (1995) Posttranscriptionally modified nucleosides in transfer RNA: their locations and frequencies. Biochimie 77:139-141

    Article  Google Scholar 

  • 55. Gutgsell NS, Del Campo MD, Raychaudhuri S, Ofengand J (2001) A second function for pseudouridine synthases: A point mutant of RluD unable to form pseudouridines 1911, 1915, and 1917 in Escherichia coli 23S ribosomal RNA restores normal growth to an RluD-minus strain. RNA 7:990-998

    Article  Google Scholar 

  • 56. Hamma T, Ferre-D’Amare AR (2004) Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 A resolution. Structure (Camb) 12:893-903

    Google Scholar 

  • 57. Heiss NS, Knight SW, Vulliamy TJ, Klauck SM, Wiemann S, Mason PJ, Poustka A, Dokal I (1998) X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions. Nat Genet 19:32-38

    CAS  PubMed  Google Scholar 

  • 58. Henras A, Dez C, Noaillac-Depeyre J, Henry Y, Caizergues-Ferrer M (2001) Accumulation of H/ACA snoRNPs depends on the integrity of the conserved central domain of the RNA-binding protein Nhp2p. Nucleic Acids Res 29:2733-2746

    Google Scholar 

  • 59. Henras A, Henry Y, Bousquet-Antonelli C, Noaillac-Depeyre J, Gélugne JP, Caizergues-Ferrer M (1998) Nhp2p and Nop10p are essential for the function of H/ACA snoRNPs. EMBO J 17:7078-7090

    Google Scholar 

  • 60. Henras AK, Capeyrou R, Henry Y, Caizergues-Ferrer M (2004) Cbf5p, the putative pseu-douridine synthase of H/ACA-type snoRNPs, can form a complex with Gar1p and Nop10p in absence of Nhp2p and box H/ACA snoRNAs. RNA 10:1704-1712

    Google Scholar 

  • 61. Hodnett JL, Busch H (1968) Isolation and characterization of uridylic acid-rich 7 S ribonu-cleic acid of rat liver nuclei. J Biol Chem 243:6334-6342

    Google Scholar 

  • 62. Hopper AK, Phizicky EM (2003) tRNA transfers to the limelight. Genes Dev 17:162-180

    Article  Google Scholar 

  • 63. Huang ZP, Zhou H, Liang D, Qu LH (2004) Different expression strategy: multiple intronic gene clusters of box H/ACA snoRNA in Drosophila melanogaster. J Mol Biol 341:669-683

    Google Scholar 

  • 64. Huttenhofer A, Brosius J, Bachellerie JP (2002) RNomics: identification and function of small, non-messenger RNAs. Curr Opin Chem Biol 6:835-843

    Google Scholar 

  • 65. Huttenhofer A, Cavaille J, Bachellerie JP (2004) Experimental RNomics: a global approach to identifying small nuclear RNAs and their targets in different model organisms. Methods Mol Biol 265:409-428

    Google Scholar 

  • 66. Huttenhofer A, Kiefmann M, Meier-Ewert S, O’Brien J, Lehrach H, Bachellerie JP, Brosius J (2001) RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO J 20:2943-2953

    Google Scholar 

  • 67. Jady BE, Bertrand E, Kiss T (2004) Human telomerase RNA and box H/ACA scaRNAs share a common Cajal body-specific localization signal. J Cell Biol 164:647-652

    Google Scholar 

  • 68. Jady BE, Kiss T (2001) A small nucleolar guide RNA functions both in 2’-O-ribose methy-lation and pseudouridylation of the U5 spliceosomal RNA. EMBO J 20:541-551

    Article  Google Scholar 

  • 69. Kass S, Tyc K, Steitz JA, Sollner-Webb B (1990) The U3 small nucleolar ribonucleopro-tein functions in the first step of preribosomal RNA processing. Cell 60:897-908

    Google Scholar 

  • 70. King TH, Liu B, McCully RR, Fournier MJ (2003) Ribosome structure and activity are al-tered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center. Mol Cell 11:425-435

    Article  Google Scholar 

  • 71. Kiss AM, Jady BE, Bertrand E, Kiss T (2004) Human box H/ACA pseudouridylation guide RNA machinery. Mol Cell Biol 24:5797-5807

    Google Scholar 

  • 72. Kiss AM, Jady BE, Darzacq X, Verheggen C, Bertrand E, Kiss T (2002) A Cajal body-specific pseudouridylation guide RNA is composed of two box H/ACA snoRNA-like domains. Nucleic Acids Res 30:4643-4649

    Article  Google Scholar 

  • 73. Kiss T (2001) Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J 20:3617-3622

    Google Scholar 

  • 74. Kiss T (2002) Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109:145-148

    Google Scholar 

  • 75. Kiss T, Jady BE (2004) Functional characterization of 2’-O-methylation and pseudouridyla-tion guide RNAs. Methods Mol Biol 265:393-408

    Google Scholar 

  • 76. Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T (1996) Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85:1077-1088

    Article  Google Scholar 

  • 77. Kiss-László Z, Henry Y, Kiss T (1998) Sequence and structural elements of methylation guide snoRNAs essential for site-specific ribose methylation of pre-rRNA. EMBO J 17:797-807

    Google Scholar 

  • 78. Klein DJ, Schmeing TM, Moore PB, Steitz TA (2001) The kink-turn: a new RNA secon-dary structure motif. EMBO J 20:4214-4221

    Google Scholar 

  • 79. Klein RJ, Misulovin Z, Eddy SR (2002) Noncoding RNA genes identified in AT-rich hy-perthermophiles. Proc Natl Acad Sci USA 99:7542-7547

    Google Scholar 

  • 80. Koonin EV (1996) Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases. Nucleic Ac-ids Res 24:2411-2415

    Google Scholar 

  • 81. Kuhn JF, Tran EJ, Maxwell ES (2002) Archaeal ribosomal protein L7 is a functional ho-molog of the eukaryotic 15.5kD/Snu13p snoRNP core protein. Nucleic Acids Res 30:931-941

    Google Scholar 

  • 82. Lafontaine DL, Tollervey D (1998) Birth of the snoRNPs: the evolution of the modifica-tion-guide snoRNAs. Trends Biochem Sci 23:383-388

    Google Scholar 

  • 83. Lafontaine DL, Tollervey D (2000) Synthesis and assembly of the box C+D small nucleolar RNPs. Mol Cell Biol 20:2650-2659

    Google Scholar 

  • 84. Lafontaine DLJ, Tollervey D (1999) Nop58p is a common component of the box C+D snoRNPs that is required for snoRNA stability. RNA 5:455-467

    Google Scholar 

  • 85. Leverette RD, Andrews MT, Maxwell ES (1992) Mouse U14 snRNA is a processed intron of the cognate hsc70 heat shock pre-messenger RNA. Cell 71:1215-1221

    Google Scholar 

  • 86. Li HD, Zagorski J, Fournier MJ (1990) Depletion of U14 small nuclear RNA (snR128) dis-rupts production of 18S rRNA in Saccharomyces cerevisiae. Mol Cell Biol 10:1145-1152

    Google Scholar 

  • 87. Liang XH, Xu YX, Michaeli S (2002) The spliced leader-associated RNA is a trypano-some-specific sn(o) RNA that has the potential to guide pseudouridine formation on the SL RNA. RNA 8:237-246

    Google Scholar 

  • 88. Liu J, Maxwell ES (1990) Mouse U14 snRNA is encoded in an intron of the mouse cognate hsc70 heat shock gene. Nucleic Acids Res 18:6565-6571

    Google Scholar 

  • 89. Lowe TM, Eddy SR (1999) A computational screen for methylation guide snoRNAs in yeast. Science 283:1168-1171

    Google Scholar 

  • 90. Lubben B, Fabrizio P, Kastner B, Luhrmann R (1995) Isolation and characterization of the small nucleolar ribonucleoprotein particle snR30 from Saccharomyces cerevisiae. J Biol Chem 270:11549-11554

    Google Scholar 

  • 91. Lukowiak AA, Narayanan A, Li ZH, Terns RM, Terns MP (2001) The snoRNA domain of vertebrate telomerase RNA functions to localize the RNA within the nucleus. RNA 7:1833-1844

    Google Scholar 

  • 92. Ma X, Zhao X, Yu YT (2003) Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism. EMBO J 22:1889-1897

    Article  Google Scholar 

  • 93. Maden BE (1990) The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog Nucleic Acid Res Mol Biol 39:241-303

    Google Scholar 

  • 94. Makarova OV, Makarov EM, Liu S, Vornlocher HP, Luhrmann R (2002) Protein 61K, en-coded by a gene (PRPF31) linked to autosomal dominant retinitis pigmentosa, is re-quired for U4/U6*U5 tri-snRNP formation and pre-mRNA splicing. EMBO J 21:1148-1157

    Google Scholar 

  • 95. Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P, Bachellerie JP, Brosius J, Huttenhofer A (2002) Experimental RNomics: identification of 140 candi-dates for small non-messenger RNAs in the plant Arabidopsis thaliana. Curr Biol 12:2002-2013

    Google Scholar 

  • 96. Marrone A, Mason PJ (2003) Dyskeratosis congenita. Cell Mol Life Sci 60:507-517

    Article  CAS  PubMed  Google Scholar 

  • 97. Martin JL, McMillan FM (2002) SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold. Curr Opin Struct Biol 12:783-793

    Google Scholar 

  • 98. Maser RL, Calvet JP (1989) U3 small nuclear RNA can be psoralen-cross-linked in vivo to the 5’ external transcribed spacer of pre-ribosomal-RNA. Proc Natl Acad Sci USA 86:6523-6527

    Google Scholar 

  • 99. Massenet S, Motorin Y, Lafontaine DL, Hurt EC, Grosjean H, Branlant C (1999) Pseu-douridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. Mol Cell Biol 19:2142-2154

    Google Scholar 

  • 100. Massenet S, Mougin A, C. B (1998) Posttranscriptional modifications in the U small nu-clear RNAs. In: Grosjean H (ed) Modification and Editing of RNA. ASM Press, Wash-ington, DC, pp 201-228

    Google Scholar 

  • 101. Maxwell ES, Fournier MJ (1995) The small nucleolar RNAs. Annu Rev Biochem 64:897-934

    Article  CAS  PubMed  Google Scholar 

  • 102. Maxwell ES, Martin TE (1986) A low-molecular-weight RNA from mouse ascites cells that hybridizes to both 18S rRNA and mRNA sequences. Proc Natl Acad Sci USA 83:7261-7265

    Google Scholar 

  • 103. McPheeters DS, Abelson J (1992) Mutational analysis of the yeast U2 snRNA suggests a structural similarity to the catalytic core of group I introns. Cell 71:819-831

    Google Scholar 

  • 104. McPheeters DS, Fabrizio P, Abelson J (1989) In vitro reconstitution of functional yeast U2 snRNPs. Genes Dev 3:2124-2136

    Google Scholar 

  • 105. Meier UT (2003) Dissecting dyskeratosis. Nat Genet 33:116-117

    Google Scholar 

  • 106. Mitchell JR, Cheng J, Collins K (1999a) A box H/ACA small nucleolar RNA-like domain at the human telomerase RNA 3’ end. Mol Cell Biol 19:567-576

    CAS  PubMed  Google Scholar 

  • 107. Mitchell JR, Wood E, Collins K (1999b) A telomerase component is defective in the human disease dyskeratosis congenita. Nature 402:551-555

    Article  CAS  PubMed  Google Scholar 

  • 108. Moore T, Zhang Y, Fenley MO, Li H (2004) Molecular basis of box C/D RNA-protein in-teractions; cocrystal structure of archaeal L7Ae and a box C/D RNA. Structure (Camb) 12:807-818

    Google Scholar 

  • 109. Motorin Y, Grosjean H (1998) Chemical structures and classification of posttranscription-ally modified nucleotides in RNA. In: Grosjean H, Benne R (eds) Modification and Editing of RNA. ASM Press, Washington, DC, pp 543-549

    Google Scholar 

  • 110. Newby MI, Greenbaum NL (2001) A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch-site architecture. RNA 7:833-845

    Article  Google Scholar 

  • 111. Newby MI, Greenbaum NL (2002) Sculpting of the spliceosomal branch site recognition motif by a conserved pseudouridine. Nat Struct Biol 9:958-965

    Article  Google Scholar 

  • 112. Ni J, Tien AL, Fournier MJ (1997) Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell 89:565-573

    Article  Google Scholar 

  • 113. Nieuwlandt DT, Carr MB, Daniels CJ (1993) In vivo processing of an intron-containing ar-chael tRNA. Mol Microbiol 8:93-99

    Google Scholar 

  • 114. Noon KR, Bruenger E, McCloskey JA (1998) Posttranscriptional modifications in 16S and 23S rRNAs of the archaeal hyperthermophile Sulfolobus solfataricus. J Bacteriol 180:2883-2888

    Google Scholar 

  • 115. Ochs RL, Lischwe MA, Spohn WH, Busch H (1985) Fibrillarin: a new protein of the nu-cleolus identified by autoimmune sera. Biol Cell 54:123-133

    Google Scholar 

  • 116. Ofengand J (2002) Ribosomal RNA pseudouridines and pseudouridine synthases. FEBS Lett 514:17-25

    Article  Google Scholar 

  • 117. Ofengand J, Fournier M (1998) The pseudouridine residues of rRNA: number, location, biosynthesis, and function. In: Grosjean H, Benne R (eds) Modification and Editing of RNA. ASM Press, Washington, DC, pp 229-253

    Google Scholar 

  • 118. Olivas WM, Muhlrad D, Parker R (1997) Analysis of the yeast genome: identification of new non-coding and small ORF-containing RNAs. Nucleic Acids Res 25:4619-4625

    Google Scholar 

  • 119. Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP (2000) Homologs of small nucleolar RNAs in Archaea. Science 288:517-522

    Google Scholar 

  • 120. Omer AD, Ziesche S, Decatur WA, Fournier MJ, Dennis PP (2003) RNA-modifying ma-chines in archaea. Mol Microbiol 48:617-629

    Article  Google Scholar 

  • 121. Omer AD, Ziesche S, Ebhardt H, Dennis PP (2002) In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex. Proc Natl Acad Sci USA 99:5289-5294

    Google Scholar 

  • 122. Pan ZQ, Ge H, Fu XY, Manley JL, Prives C (1989) Oligonucleotide-targeted degradation of U1 and U2 snRNAs reveals differential interactions of simian virus 40 pre-mRNAs with snRNPs. Nucleic Acids Res 17:6553-6568

    Google Scholar 

  • 123. Peculis B (1997) RNA processing: pocket guides to ribosomal RNA. Curr Biol 7:R480-482

    Google Scholar 

  • 124. Pelczar P, Filipowicz W (1998) The host gene for intronic U17 small nucleolar RNAs in mammals has no protein-coding potential and is a member of the 5’-terminal oli-gopyrimidine gene family. Mol Cell Biol 18:4509-4518

    Google Scholar 

  • 125. Pogacic V, Dragon F, Filipowicz W (2000) Human H/ACA small nucleolar RNPs and te-lomerase share evolutionarily conserved proteins NHP2 and NOP10. Mol Cell Biol 20:9028-9040

    Article  CAS  PubMed  Google Scholar 

  • 126. Qu LH, Henras A, Lu YJ, Zhou H, Zhou WX, Zhu YQ, Zhao J, Henry Y, Caizergues-Ferrer M, Bachellerie JP (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

    Google Scholar 

  • 127. Qu LH, Meng Q, Zhou H, Chen YQ, Liang-Hu Q, Qing M, Hui Z, Yue-Qin C (2001) Iden-tification of 10 novel snoRNA gene clusters from Arabidopsis thaliana. Nucleic Acids Res 29:1623-1630

    Google Scholar 

  • 128. Rashid R, Aittaleb M, Chen Q, Spiegel K, Demeler B, Li H (2003) Functional requirement for symmetric assembly of archaeal box C/D small ribonucleoprotein particles. J Mol Biol 333:295-306

    Google Scholar 

  • 129. Raychaudhuri S, Conrad J, Hall BG, Ofengand J (1998) A pseudouridine synthase required for the formation of two universally conserved pseudouridines in ribosomal RNA is essential for normal growth of Escherichia coli. RNA 4:1407-1417

    Google Scholar 

  • 130. Reddy R, Busch H (1988) Small nuclear RNAs: RNA sequences, structure, and modifica-tions. In: Birnsteil ML (ed) Structure and function of major and minor small nuclear ribonucleoprotein particles. Sringer-Verlag Press, Heidelberg, pp 1-37

    Google Scholar 

  • 131. Rimoldi OJ, Raghu B, Nag MK, Eliceiri GL (1993) Three new small nucleolar RNAs that are psoralen cross-linked in vivo to unique regions of pre-rRNA. Mol Cell Biol 13:4382-4390

    Google Scholar 

  • 132. Rozhdestvensky TS, Tang TH, Tchirkova IV, Brosius J, Bachellerie JP, Huttenhofer A (2003) Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. Nucleic Acids Res 31:869-877

    Google Scholar 

  • 133. Ruff EA, Rimoldi OJ, Raghu B, Eliceiri GL (1993) Three small nucleolar RNAs of unique nucleotide sequences. Proc Natl Acad Sci USA 90:635-638

    Google Scholar 

  • 134. Ruggero D, Grisendi S, Piazza F, Rego E, Mari F, Rao PH, Cordon-Cardo C, Pandolfi PP (2003) Dyskeratosis congenita and cancer in mice deficient in ribosomal RNA modifi-cation. Science 299:259-262

    Article  CAS  PubMed  Google Scholar 

  • 135. Samarsky DA, Fournier MJ (1999) A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae. Nucleic Acids Res 27:161-164

    Google Scholar 

  • 136. Schattner P, Decatur WA, Davis CA, Ares M Jr, Fournier MJ, Lowe TM (2004) Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Res 32:4281-4296

    Google Scholar 

  • 137. Schubert HL, Blumenthal RM, Cheng X (2003) Many paths to methyltransfer: a chronicle of convergence. Trends Biochem Sci 28:329-335

    Google Scholar 

  • 138. Segault V, Will CL, Sproat BS, Luhrmann R (1995) In vitro reconstitution of mammalian U2 and U5 snRNPs active in splicing: Sm proteins are functionally interchangeable and are essential for the formation of functional U2 and U5 snRNPs. EMBO J 14:4010-4021

    Google Scholar 

  • 139. Singh SK, Gurha P, Tran EJ, Maxwell ES, Gupta R (2004) A trans mechanism for archaeal tRNAtrp nucleotide 2’-O-methylation guided by the pre-tRNATrp intron-encoded box C/D RNPs. The 2004 RNA meeting abstract:744

    Google Scholar 

  • 140. Smith CM, Steitz JA (1997) Sno storm in the nucleolus: new roles for myriad small RNPs. Cell 89:669-672

    Google Scholar 

  • 141. Smith CM, Steitz JA (1998) Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene and a member of the 5’-terminal oligopyrimidine gene family re-veals common features of snoRNA host genes. Mol Cell Biol 18:6897-6909

    Google Scholar 

  • 142. Speckmann WA, Li ZH, Lowe TM, Eddy SR, Terns RM, Terns MP (2002) Archaeal guide RNAs function in rRNA modification in the eukaryotic nucleus. Curr Biol 12:199-203

    Google Scholar 

  • 143. Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S (1998) Compilation of tRNA se-quences and sequences of tRNA genes. Nucleic Acids Res 26:148-153

    Article  Google Scholar 

  • 144. Starostina NG, Marshburn S, Johnson LS, Eddy SR, Terns RM, Terns MP (2004) Circular box C/D RNAs in Pyrococcus furiosus. Proc Natl Acad Sci USA 101:14097-14101

    Google Scholar 

  • 145. Steitz JA, Tycowski KT (1995) Small RNA chaperones for ribosome biogenesis. Science 270:1626-1627

    Google Scholar 

  • 146. Stroke IL, Weiner AM (1989) The 5’ end of U3 snRNA can be crosslinked in vivo to the external transcribed spacer of rat ribosomal RNA precursors. J Mol Biol 210:497-512

    Google Scholar 

  • 147. Szewczak LB, DeGregorio SJ, Strobel SA, Steitz JA (2002) Exclusive interaction of the 15.5 kD protein with the terminal box C/D motif of a methylation guide snoRNP. Chem Biol 9:1095-1107

    Google Scholar 

  • 148. Tang TH, Bachellerie JP, Rozhdestvensky T, Bortolin ML, Huber H, Drungowski M, Elge T, Brosius J, Huttenhofer A (2002) Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc Natl Acad Sci USA 99:7536-7541

    Google Scholar 

  • 149. Terns MP, Terns RM (2002) Small nucleolar RNAs: versatile trans-acting molecules of an-cient evolutionary origin. Gene Expr 10:17-39

    Google Scholar 

  • 150. Tollervey D, Lehtonen H, Carmo-Fonseca M, Hurt EC (1991) The small nucleolar RNP protein NOP1 (fibrillarin) is required for pre-rRNA processing in yeast. EMBO J 10:573-583

    Google Scholar 

  • 151. Tollervey D, Lehtonen H, Jansen R, Kern H, Hurt EC (1993) Temperature-sensitive muta-tions demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methy-lation, and ribosome assembly. Cell 72:443-457

    Google Scholar 

  • 152. Tran E, Brown J, Maxwell ES (2004) Evolutionary origins of the RNA-guided nucleotide-modification complexes: from the primitive translation apparatus? Trends Biochem Sci 29:343-350

    Article  Google Scholar 

  • 153. Tran EJ, Zhang X, Maxwell ES (2003) Efficient RNA 2’-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C’/D’ RNPs. EMBO J. 22:3930-3940

    Google Scholar 

  • 154. Trinh-Rohlik Q, Maxwell ES (1988) Homologous genes for mouse 4.5S hybRNA are found in all eukaryotes and their low molecular weight RNA transcripts intermolecularly hy-bridize with eukaryotic 18S ribosomal RNAs. Nucleic Acids Res 16:6041-6056

    Google Scholar 

  • 155. Tyc K, Steitz JA (1989) U3, U8 and U13 comprise a new class of mammalian snRNPs lo-calized in the cell nucleolus. EMBO J 8:3113-3119

    Google Scholar 

  • 156. Tycowski KT, Shu MD, Steitz JA (1996) A mammalian gene with introns instead of exons generating stable RNA products. Nature 379:464-466

    Google Scholar 

  • 157. Tycowski KT, Steitz JA (2001) Non-coding snoRNA host genes in Drosophila: expression strategies for modification guide snoRNAs. Eur J Cell Biol 80:119-125

    Google Scholar 

  • 158. Tycowski KT, You ZH, Graham PJ, Steitz JA (1998) Modification of U6 spliceosomal RNA is guided by other small RNAs. Mol Cell 2:629-638

    Google Scholar 

  • 159. Uliel S, Liang XH, Unger R, Michaeli S (2004) Small nucleolar RNAs that guide modifica-tion in trypanosomatids: repertoire, targets, genome organisation, and unique func-tions. Int J Parasitol 34:445-454

    Google Scholar 

  • 160. Valadkhan S, Manley JL (2003) Characterization of the catalytic activity of U2 and U6 snRNAs. RNA 9:892-904

    Article  Google Scholar 

  • 161. Vidovic I, Nottrott S, Hartmuth K, Luhrmann R, Ficner R (2000) Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment. Mol Cell 6:1331-1342

    Google Scholar 

  • 162. Villa T, Ceradini F, Presutti C, Bozzoni I (1998) Processing of the intron-encoded U18 small nucleolar RNA in the yeast Saccharomyces cerevisiae relies on both exo- and endonucleolytic activities. Mol Cell Biol 18:3376-3383

    Google Scholar 

  • 163. Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J (2003) Identification of 13 novel human modification guide RNAs. Nucleic Acids Res 31:6543-6551

    Google Scholar 

  • 164. Wang C, Meier UT (2004) Architecture and assembly of mammalian H/ACA small nucleo-lar and telomerase ribonucleoproteins. EMBO J 23:1857-1867

    Google Scholar 

  • 165. Wang C, Query CC, Meier UT (2002) Immunopurified small nucleolar ribonucleoprotein particles pseudouridylate rRNA independently of their association with phosphorylated Nopp140. Mol Cell Biol 22:8457-8466

    Google Scholar 

  • 166. Wang H, Boisvert D, Kim KK, Kim R, Kim SH (2000) Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution. EMBO J 19:317-323

    Google Scholar 

  • 167. Watanabe Y, Gray MW (2000) Evolutionary appearance of genes encoding proteins associ-ated with box H/ACA snoRNAs: cbf5p in Euglena gracilis, an early diverging eu-karyote, and candidate Gar1p and Nop10p homologs in archaebacteria. Nucleic Acids Res 28:2342-2352

    Google Scholar 

  • 168. Watkins KP, Dungan JM, Agabian N (1994) Identification of a small RNA that interacts with the 5’ splice site of the Trypanosoma brucei spliced leader RNA in vivo. Cell T6:171-182

    Google Scholar 

  • 169. Watkins NJ, Gottschalk A, Neubauer G, Kastner B, Fabrizio P, Mann M, Lührmann 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 snoRNPs and con-stitute a common bipartite structure. RNA 4:1549-1568

    Google Scholar 

  • 170. Watkins NJ, Segault V, Charpentier B, Nottrott S, Fabrizio P, Bachi A, Wilm M, Rosbash M, Branlant C, 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

    Google Scholar 

  • 171. Weidenhammer EM, Ruiz-Noriega M, Woolford JL Jr (1997) Prp31p promotes the associa-tion of the U4/U6 x U5 tri-snRNP with prespliceosomes to form spliceosomes in Sac-charomyces cerevisiae. Mol Cell Biol 17:3580-3588

    Google Scholar 

  • 172. Wise JA, Tollervey D, Maloney D, Swerdlow H, Dunn EJ, Guthrie C (1983) Yeast contains small nuclear RNAs encoded by single copy genes. Cell 35:743-751

    Google Scholar 

  • 173. Yu YT, Scharl EC, Smith CM, Steitz JA (1999) The growing world of small nuclear ribo-nucleoproteins. In: Gesteland RF, Cech TR, Atkins JF (eds) The RNA world, 2nd edn. Cold Spring Harbor laboratory Press, Cold Spring Harbor, New York, pp 487-524

    Google Scholar 

  • 174. Yu YT, Shu MD, Steitz JA (1997) A new method for detecting sites of 2’-O-methylation in RNA molecules. RNA 3:324-331

    Google Scholar 

  • 175. Yu YT, Shu MD, Steitz JA (1998) Modifications of U2 snRNA are required for snRNP as-sembly and pre-mRNA splicing. EMBO J 17:5783-5795

    Article  Google Scholar 

  • 176. Yuan G, Klambt C, Bachellerie JP, Brosius J, Huttenhofer A (2003) RNomics in Droso-phila melanogaster: identification of 66 candidates for novel non-messenger RNAs. Nucleic Acids Res 31:2495-2507

    Google Scholar 

  • 177. Zagorski J, Tollervey D, Fournier MJ (1988) Characterization of an SNR gene locus in Saccharomyces cerevisiae that specifies both dispensable and essential small nuclear RNAs. Mol Cell Biol 8:3282-3290

    Google Scholar 

  • 178. Zebarjadian Y, King T, Fournier MJ, Clarke L, Carbon J (1999) Point mutations in yeast CBF5 can abolish in vivo pseudouridylation of rRNA. Mol Cell Biol 19:7461-7472

    Google Scholar 

  • 179. Zhao X, Li ZH, Terns RM, Terns MP, Yu YT (2002) An H/ACA guide RNA directs U2 pseudouridylation at two different sites in the branchpoint recognition region in Xenopus oocytes. RNA 8:1515-1525

    Google Scholar 

  • 180. Zhao X, Yu YT (2004a) Detection and quantitation of RNA base modifications. RNA 10:996-1002

    Google Scholar 

  • 181. Zhao X, Yu YT (2004b) Pseudouridines in and near the branch site recognition region of U2 snRNA are required for snRNP biogenesis and pre-mRNA splicing in Xenopus oo-cytes. RNA 10:681-690

    Article  Google Scholar 

  • 182. Zhu Y, Tomlinson RL, Lukowiak AA, Terns RM, Terns MP (2004) Telomerase RNA ac-cumulates in Cajal bodies in human cancer cells. Mol Biol Cell 15:81-90

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Yi-Tao Yu .

Editor information

Henri Grosjean

Rights and permissions

Reprints and permissions

About this chapter

Cite this chapter

Yu, YT., Terns, R.M., Terns, M.P. Mechanisms and functions of RNA-guided RNA modification. In: Grosjean, H. (eds) Fine-Tuning of RNA Functions by Modification and Editing. Topics in Current Genetics, vol 12. Springer, Berlin, Heidelberg. https://doi.org/10.1007/b105585

Download citation

Publish with us

Policies and ethics