Small nucleolar RNAs

Abstract. Many small RNA species associate with the nucleolar structure. Some of these small nucleolar RNAs (snoRNAs) are required for cleavage processing of ribosomal RNA precursors. There are many pseudouridine residues and methylated riboses in mature ribosomal RNA. For most, if not all, of these modifications, each site is selected by base pairing with a specific snoRNA species. Some snoRNAs are needed for the 2′-O-ribose methylation of at least one spliceosomal small nuclear RNA. Many snoRNAs, particularly in yeast, are generated from independent transcription units. Most vertebrate snoRNAs are produced by processing of introns from protein-coding transcripts. Some snoRNAs are made by processing of introns from non-protein-coding transcripts.

[1]  W. Filipowicz,et al.  Small nucleolar RNAs encoded by introns of the human cell cycle regulatory gene RCC1. , 1993, The EMBO journal.

[2]  J. Bachellerie,et al.  Guiding ribose methylation of rRNA. , 1997, Trends in biochemical sciences.

[3]  M. Ares,et al.  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. , 1991, The EMBO journal.

[4]  D. Tollervey,et al.  The yeast Hansenula wingei U3 snoRNA gene contains an intron and its coding sequence co-evolved with the 5' ETS region of the pre-ribosomal RNA. , 1996, RNA: A publication of the RNA Society.

[5]  E. Maxwell,et al.  In vitro assembly of the mouse U14 snoRNP core complex and identification of a 65-kDa box C/D-binding protein. , 1998, RNA.

[6]  D. Tollervey,et al.  Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis , 1993, Molecular and cellular biology.

[7]  William Arbuthnot Sir Lane,et al.  Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. , 1998, Genes & development.

[8]  J. Bachellerie,et al.  Processing of fibrillarin-associated snoRNAs from pre-mRNA introns: an exonucleolytic process exclusively directed by the common stem-box terminal structure. , 1996, Biochimie.

[9]  J. Hughes,et al.  Functional base-pairing interaction between highly conserved elements of U3 small nucleolar RNA and the small ribosomal subunit RNA. , 1996, Journal of molecular biology.

[10]  P. Mitchell,et al.  The 3' end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism. , 1996, Genes & development.

[11]  D. Tollervey,et al.  RRP5 is required for formation of both 18S and 5.8S rRNA in yeast. , 1996, The EMBO journal.

[12]  D. Engelke,et al.  An RNase P RNA subunit mutation affects ribosomal RNA processing. , 1996, Nucleic acids research.

[13]  Maurille J. Fournier,et al.  The Pseudouridine Residues of rRNA: Number, Location, Biosynthesis, and Function , 1998 .

[14]  M. Mann,et al.  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 constitute a common bipartite structure. , 1998, RNA.

[15]  J. Steitz,et al.  U3, U8 and U13 comprise a new class of mammalian snRNPs localized in the cell nucleolus. , 1989, The EMBO journal.

[16]  G. L. Eliceiri,et al.  Three new small nucleolar RNAs that are psoralen cross-linked in vivo to unique regions of pre-rRNA , 1993, Molecular and cellular biology.

[17]  D. Tollervey,et al.  Trans-acting factors in yeast pre-rRNA and pre-snoRNA processing. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[18]  J. Bachellerie,et al.  Small Nucleolar RNAs Guide the Ribose Methylations of Eukaryotic rRNAs , 1998 .

[19]  J. Ni,et al.  Small Nucleolar RNAs Direct Site-Specific Synthesis of Pseudouridine in Ribosomal RNA , 1997, Cell.

[20]  M. Fournier,et al.  An essential domain in Saccharomyces cerevisiae U14 snoRNA is absent in vertebrates, but conserved in other yeasts. , 1996, Nucleic acids research.

[21]  R. Singer,et al.  The snoRNA box C/D motif directs nucleolar targeting and also couples snoRNA synthesis and localization , 1998, The EMBO journal.

[22]  Tamás Kiss,et al.  Elements essential for accumulation and function of small nucleolar RNAs directing site‐specific pseudouridylation of ribosomal RNAs , 1999, The EMBO journal.

[23]  G. L. Eliceiri,et al.  Three small nucleolar RNAs of unique nucleotide sequences. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[24]  M. Terns,et al.  Retention and 5' cap trimethylation of U3 snRNA in the nucleus. , 1994, Science.

[25]  N Selvamurugan,et al.  Genes for E1, E2, and E3 small nucleolar RNAs. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[26]  James R. Cole,et al.  A new version of the RDP (Ribosomal Database Project) , 1999, Nucleic Acids Res..

[27]  P. Linder,et al.  Dbp7p, a putative ATP-dependent RNA helicase from Saccharomyces cerevisiae, is required for 60S ribosomal subunit assembly. , 1998, RNA.

[28]  R. Lührmann,et al.  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. , 1997, Journal of molecular biology.

[29]  J. Liu,et al.  Mouse U14 snRNA is encoded in an intron of the mouse cognate hsc70 heat shock gene. , 1990, Nucleic acids research.

[30]  J. Steitz,et al.  Classification of gas5 as a Multi-Small-Nucleolar-RNA (snoRNA) Host Gene and a Member of the 5′-Terminal Oligopyrimidine Gene Family Reveals Common Features of snoRNA Host Genes , 1998, Molecular and Cellular Biology.

[31]  W. Filipowicz,et al.  Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns. , 1995, Genes & development.

[32]  S. Baserga,et al.  Functional separation of pre-rRNA processing steps revealed by truncation of the U3 small nucleolar ribonucleoprotein component, Mpp10. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[33]  J. Steitz,et al.  Disruption of U8 nucleolar snRNA inhibits 5.8S and 28S rRNA processing in the Xenopus oocyte , 1993, Cell.

[34]  S. Baserga,et al.  Mpp10p, a U3 small nucleolar ribonucleoprotein component required for pre-18S rRNA processing in yeast , 1997, Molecular and cellular biology.

[35]  J. Boeke,et al.  Intronic snoRNA biosynthesis in Saccharomyces cerevisiae depends on the lariat-debranching enzyme: intron length effects and activity of a precursor snoRNA. , 1998, RNA.

[36]  I. Bozzoni,et al.  A novel small nucleolar RNA (U16) is encoded inside a ribosomal protein intron and originates by processing of the pre‐mRNA. , 1993, The EMBO journal.

[37]  N. Selvamurugan,et al.  The gene for human E2 small nucleolar RNA resides in an intron of a laminin-binding protein gene. , 1995, Genomics.

[38]  J. Steitz,et al.  Sequence and structural elements critical for U8 snRNP function in Xenopus oocytes are evolutionarily conserved. , 1994, Genes & development.

[39]  Raghvendra Kumar Mishra,et al.  Three small nucleolar RNAs that are involved in ribosomal RNA precursor processing. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Laurie Smith,et al.  The RNA World of the Nucleolus: Two Major Families of Small RNAs Defined by Different Box Elements with Related Functions , 1996, Cell.

[41]  W. Filipowicz,et al.  The Host Gene for Intronic U17 Small Nucleolar RNAs in Mammals Has No Protein-Coding Potential and Is a Member of the 5′-Terminal Oligopyrimidine Gene Family , 1998, Molecular and Cellular Biology.

[42]  D. Tollervey,et al.  The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. , 1998, Genes & development.

[43]  M. Fournier,et al.  Functional Mapping of the U3 Small Nucleolar RNA from the Yeast Saccharomyces cerevisiae , 1998, Molecular and Cellular Biology.

[44]  J. Steitz,et al.  A small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein S3. , 1993, Genes & Development.

[45]  B. Séraphin,et al.  Accurate Processing of a Eukaryotic Precursor Ribosomal RNA by Ribonuclease MRP in Vitro , 1996, Science.

[46]  J. Bachellerie,et al.  SnoRNA-guided ribose methylation of rRNA: structural features of the guide RNA duplex influencing the extent of the reaction. , 1998, Nucleic acids research.

[47]  J. Steitz,et al.  A mammalian gene with introns instead of exons generating stable RNA products , 1996, Nature.

[48]  T. Kiss,et al.  The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. , 1997, Genes & development.

[49]  Tamás Kiss,et al.  Site-Specific Ribose Methylation of Preribosomal RNA: A Novel Function for Small Nucleolar RNAs , 1996, Cell.

[50]  D A Clayton,et al.  Nuclear RNase MRP is required for correct processing of pre-5.8S rRNA in Saccharomyces cerevisiae , 1993, Molecular and cellular biology.

[51]  M. Terns,et al.  A common maturation pathway for small nucleolar RNAs. , 1995, The EMBO journal.

[52]  M. Fournier,et al.  The nucleolar snRNAs: catching up with the spliceosomal snRNAs. , 1993, Trends in biochemical sciences.

[53]  M. W. Clark,et al.  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 , 1990, The Journal of cell biology.

[54]  D. Tollervey,et al.  Base pairing between U3 and the pre‐ribosomal RNA is required for 18S rRNA synthesis. , 1995, The EMBO journal.

[55]  J. Steitz,et al.  A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[56]  Y. Wang,et al.  Dynamic localization of RNase MRP RNA in the nucleolus observed by fluorescent RNA cytochemistry in living cells , 1995, The Journal of cell biology.

[57]  M. Bortolin,et al.  Human U19 intron-encoded snoRNA is processed from a long primary transcript that possesses little potential for protein coding. , 1998, RNA.

[58]  Jeffrey B. Cheng,et al.  A Box H/ACA Small Nucleolar RNA-Like Domain at the Human Telomerase RNA 3′ End , 1999, Molecular and Cellular Biology.

[59]  J. Steitz,et al.  ENHANCED PERSPECTIVE: Small RNA Chaperones for Ribosome Biogenesis , 1995, Science.

[60]  R. Singer,et al.  Nuclear domains of the RNA subunit of RNase P. , 1997, Journal of cell science.

[61]  P. Legrain,et al.  Processing of a dicistronic small nucleolar RNA precursor by the RNA endonuclease Rnt1 , 1998, The EMBO journal.

[62]  D. Tollervey,et al.  Yeast 18S rRNA Dimethylase Dim1p: a Quality Control Mechanism in Ribosome Synthesis? , 1998, Molecular and Cellular Biology.

[63]  S. Gerbi,et al.  Nucleolar localization elements in U8 snoRNA differ from sequences required for rRNA processing. , 1998, RNA.

[64]  M. Mann,et al.  The Exosome: A Conserved Eukaryotic RNA Processing Complex Containing Multiple 3′→5′ Exoribonucleases , 1997, Cell.

[65]  B. Maden.  The numerous modified nucleotides in eukaryotic ribosomal RNA. , 1990, Progress in nucleic acid research and molecular biology.

[66]  D. Tollervey.  A yeast small nuclear RNA is required for normal processing of pre‐ribosomal RNA. , 1987, The EMBO journal.

[67]  T. Hartshorne.  Distinct regions of U3 snoRNA interact at two sites within the 5' external transcribed spacer of pre-rRNAs in Trypanosoma brucei cells. , 1998, Nucleic acids research.

[68]  M. Fournier,et al.  Depletion of U14 small nuclear RNA (snR128) disrupts production of 18S rRNA in Saccharomyces cerevisiae. , 1990, Molecular and cellular biology.

[69]  J. Steitz,et al.  Requirement for intron-encoded U22 small nucleolar RNA in 18S ribosomal RNA maturation. , 1994, Science.

[70]  D. Tollervey,et al.  Function and synthesis of small nucleolar RNAs. , 1997, Current opinion in cell biology.

[71]  K. L. Himmel,et al.  The yeast SEN1 gene is required for the processing of diverse RNA classes. , 1997, Nucleic acids research.

[72]  E. Petfalski,et al.  Processing of the Precursors to Small Nucleolar RNAs and rRNAs Requires Common Components , 1998, Molecular and Cellular Biology.

[73]  J. Brockenbrough,et al.  Nop5p Is a Small Nucleolar Ribonucleoprotein Component Required for Pre-18 S rRNA Processing in Yeast* , 1998, The Journal of Biological Chemistry.

[74]  D. Dairaghi,et al.  Secondary structure of RNase MRP RNA as predicted by phylogenetic comparison , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[75]  L. Lindahl,et al.  The RNA of RNase MRP is required for normal processing of ribosomal RNA. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[76]  E. Maxwell,et al.  5'ETS rRNA processing facilitated by four small RNAs: U14, E3, U17, and U3. , 1996, RNA.

[77]  S. Gerbi,et al.  Nucleolar localization elements of Xenopus laevis U3 small nucleolar RNA. , 1998, Molecular biology of the cell.

[78]  A. Fatica,et al.  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. , 1996, The EMBO journal.

[79]  C. Jacq,et al.  Two mutant forms of the S1/TPR-containing protein Rrp5p affect the 18S rRNA synthesis in Saccharomyces cerevisiae. , 1998, RNA.

[80]  I. Bozzoni,et al.  In vitro study of processing of the intron-encoded U16 small nucleolar RNA in Xenopus laevis , 1994, Molecular and cellular biology.

[81]  D. Tollervey,et al.  Birth of the snoRNPs: the evolution of RNase MRP and the eukaryotic pre-rRNA-processing system. , 1995, Trends in biochemical sciences.

[82]  J. Steitz,et al.  The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing , 1990, Cell.

[83]  M. Caizergues-Ferrer,et al.  Nhp2p and Nop10p are essential for the function of H/ACA snoRNPs , 1998, The EMBO journal.

[84]  Sherif Abou Elela,et al.  RNase III Cleaves Eukaryotic Preribosomal RNA at a U3 snoRNP-Dependent Site , 1996, Cell.

[85]  D. Tollervey,et al.  Dob1p (Mtr4p) is a putative ATP‐dependent RNA helicase required for the 3′ end formation of 5.8S rRNA in Saccharomyces cerevisiae , 1998, The EMBO journal.

[86]  Tamás Kiss,et al.  Site-Specific Pseudouridine Formation in Preribosomal RNA Is Guided by Small Nucleolar RNAs , 1997, Cell.

[87]  E. Maxwell,et al.  Mouse U14 snRNA is a processed intron of the cognate hsc70 heat shock pre-messenger RNA , 1992, Cell.

[88]  J. Vandenhaute,et al.  The 18S rRNA dimethylase Dim1p is required for pre-ribosomal RNA processing in yeast. , 1995, Genes & development.

[89]  J. Steitz,et al.  Small RNA chaperones for ribosome biogenesis. , 1995, Science.

[90]  M. Fournier,et al.  U14 base-pairs with 18S rRNA: a novel snoRNA interaction required for rRNA processing. , 1995, Genes & development.

[91]  M. Culbertson,et al.  The Putative Nucleic Acid Helicase Sen1p Is Required for Formation and Stability of Termini and for Maximal Rates of Synthesis and Levels of Accumulation of Small Nucleolar RNAs inSaccharomyces cerevisiae , 1998, Molecular and Cellular Biology.

[92]  J. Bachellerie,et al.  Antisense snoRNAs: a family of nucleolar RNAs with long complementarities to rRNA. , 1995, Trends in biochemical sciences.

[93]  B. Kastner,et al.  Isolation and characterization of the small nucleolar ribonucleoprotein particle snR30 from Saccharomyces cerevisiae , 1995, The Journal of Biological Chemistry.

[94]  B. Peculis,et al.  The sequence of the 5' end of the U8 small nucleolar RNA is critical for 5.8S and 28S rRNA maturation , 1997, Molecular and cellular biology.

[95]  T. Pederson,et al.  A 7-methylguanosine cap commits U3 and U8 small nuclear RNAs to the nucleolar localization pathway. , 1998, Nucleic acids research.

[96]  J. Bachellerie,et al.  Novel intron-encoded small nucleolar RNAs with long sequence complementarities to mature rRNAs involved in ribosome biogenesis. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[97]  S. Gerbi,et al.  In vivo disruption of Xenopus U3 snRNA affects ribosomal RNA processing. , 1990, The EMBO journal.

[98]  S. Eddy,et al.  A computational screen for methylation guide snoRNAs in yeast. , 1999, Science.

[99]  E. Maxwell,et al.  Identification of specific nucleotide sequences and structural elements required for intronic U14 snoRNA processing. , 1997, RNA.

[100]  F. Cecconi,et al.  The Xenopus intron-encoded U17 snoRNA is produced by exonucleolytic processing of its precursor in oocytes. , 1995, Nucleic acids research.

[101]  D. Tollervey,et al.  Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis , 1997, Molecular and cellular biology.

[102]  S. Baserga,et al.  The U14 snoRNA is required for 2'-O-methylation of the pre-18S rRNA in Xenopus oocytes. , 1998, RNA.

[103]  J. Bachellerie,et al.  Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides , 1996, Nature.

[104]  Z. Kiss-László,et al.  Sequence and structural elements of methylation guide snoRNAs essential for site‐specific ribose methylation of pre‐rRNA , 1998, The EMBO journal.

[105]  Dmitry A. Samarsky,et al.  A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae , 1999, Nucleic Acids Res..

[106]  T. Pederson,et al.  The plurifunctional nucleolus. , 1998, Nucleic acids research.

[107]  J. Steitz,et al.  Modification of U6 spliceosomal RNA is guided by other small RNAs. , 1998, Molecular cell.

[108]  J. Steitz,et al.  Sno Storm in the Nucleolus: New Roles for Myriad Small RNPs , 1997, Cell.

[109]  D. Tollervey.  Trans-acting factors in ribosome synthesis. , 1996, Experimental Cell Research.

[110]  M. Caizergues-Ferrer,et al.  A small nucleolar RNP protein is required for pseudouridylation of eukaryotic ribosomal RNAs , 1997, The EMBO journal.

[111]  M. Fournier,et al.  The rRNA-processing function of the yeast U14 small nucleolar RNA can be rescued by a conserved RNA helicase-like protein , 1997, Molecular and cellular biology.

[112]  M. Fournier,et al.  The small nucleolar RNAs. , 1995, Annual review of biochemistry.

[113]  I. Bozzoni,et al.  Processing of the Intron-Encoded U18 Small Nucleolar RNA in the Yeast Saccharomyces cerevisiaeRelies on Both Exo- and Endonucleolytic Activities , 1998, Molecular and Cellular Biology.

[114]  E. Maxwell,et al.  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. , 1996, RNA.

[115]  J. Brown,et al.  Intracellular localization and unique conserved sequences of three small nucleolar RNAs. , 1997, Nucleic acids research.

[116]  Liang-Hu Qu,et al.  Seven Novel Methylation Guide Small Nucleolar RNAs Are Processed from a Common Polycistronic Transcript by Rat1p and RNase III in Yeast , 1999, Molecular and Cellular Biology.

[117]  J. Bachellerie,et al.  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. , 1996, Journal of molecular biology.

[118]  D. Tollervey,et al.  Rok1p is a putative RNA helicase required for rRNA processing , 1997, Molecular and cellular biology.

[119]  D. Tollervey,et al.  Spb4p, an essential putative RNA helicase, is required for a late step in the assembly of 60S ribosomal subunits in Saccharomyces cerevisiae. , 1998, RNA.

[120]  S. Gerbi,et al.  Conserved Boxes C and D are essential nucleolar localization elements of U14 and U8 snoRNAs , 1998, The EMBO journal.

[121]  P. Legrain,et al.  Yeast RNase III as a key processing enzyme in small nucleolar RNAs metabolism. , 1998, Journal of molecular biology.