[1] Arnez, J.G., and Steitz, T.A. (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 .8011621
[2] Bachellerie, J.P., Michot, B., Nicoloso, M., Balakin, A., Ni, J., and Fournier, M.J. (1995). Antisense snoRNAs: a family of nucleolar RNAs with long complementarities to rRNA.
Trends Biochem Sci 20, 261-264 .7667877
[3] Bakin, A., and Ofengand, J. (1993). Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the application of a new sequencing technique.
Biochemistry 32, 9754-9762 .8373778
[4] Balakin, A.G., Smith, L., and Fournier, M.J. (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 .8797828
[5] Behm-Ansmant, I., Urban, A., Ma, X., Yu, Y.T., Motorin, Y., and Branlant, C. (2003). The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Psi-synthase also acting on tRNAs.
RNA 9, 1371-1382 .14561887
[6] Berget, S.M., Moore, C., and Sharp, P.A. (1977). Spliced segments at the 5′ terminus of adenovirus 2 late mRNA.
Proc Natl Acad Sci U S A 74, 3171-3175 .269380
[7] Burge, C.B., Tuschl, T., and Sharp, P.A. (1999). Splicing of precursors to mRNAs by the spliceosome
. In: The RNA World . Gesteland R.F., Cech T.R., and Atkins J.F. eds.
Cold Spring Harbor:
Cold Spring Harbor Laboratory Press. 525-560 .
[8] Cavaillé, J., Nicoloso, M., and Bachellerie, J.P. (1996). Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides.
Nature 383, 732-735 .8878486
[9] Charette, M., and Gray, M.W. (2000). Pseudouridine in RNA: what, where, how, and why.
IUBMB Life 49, 341-351 .10902565
[10] Chen, C., Zhao, X., Kierzek, R., and Yu, Y.T. (2010). A flexible RNA backbone within the polypyrimidine tract is required for U2AF65 binding and pre-mRNA splicing in vivo.
Mol Cell Biol 30, 4108-4119 .20606010
[11] Cheng, S.C., and Abelson, J. (1987). Spliceosome assembly in yeast.
Genes Dev 1, 1014-1027 .2962902
[12] Chow, L.T., Gelinas, R.E., Broker, T.R., and Roberts, R.J. (1977). An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA.
Cell 12, 1-8 .902310
[13] Cohn, W.E., and Volkin, E. (1951). Nucleoside-5'-Phosphates from Ribonucleic Acid.
Nature 167, 483-484 .
[14] Cortes, J.J., Sontheimer, E.J., Seiwert, S.D., and Steitz, J.A. (1993). Mutations in the conserved loop of human U5 snRNA generate use of novel cryptic 5′ splice sites in vivo.
EMBO J 12, 5181-5189 .8262061
[15] Dai, Q., Fong, R., Saikia, M., Stephenson, D., Yu, Y.T., Pan, T., and Piccirilli, J.A. (2007). Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine.
Nucleic Acids Res 35, 6322-6329 .17881375
[16] Datta, B., and Weiner, A.M. (1991). Genetic evidence for base pairing between U2 and U6 snRNA in mammalian mRNA splicing.
Nature 352, 821-824 .1831879
[17] Davis, D.R. (1995). Stabilization of RNA stacking by pseudouridine.
Nucleic Acids Res 23, 5020-5026 .8559660
[18] Davis, F.F., and Allen, F.W. (1957). Ribonucleic acids from yeast which contain a fifth nucleotide.
J Biol Chem 227, 907-915 .13463012
[19] Del Campo, M., Ofengand, J., and Malhotra, A. (2004). Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli.
RNA 10, 231-239 .14730022
[20] Donmez, G., Hartmuth, K., and Luhrmann, R. (2004). Modified nucleotides in the 5' end of the human U2 snRNA are required for early spliceosome (E complex) formation in vitro
. The 2004 RNA Meeting abstract , 92.
[21] Duan, J., Li, L., Lu, J., Wang, W., and Ye, K. (2009). Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase.
Mol Cell 34, 427-439 .19481523
[22] Ericsson, U.B., Nordlund, P., and Hallberg, B.M. (2004). X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold.
FEBS Lett 565, 59-64 .15135053
[23] Foster, P.G., Huang, L., Santi, D.V., and Stroud, R.M. (2000). The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I.
Nat Struct Biol 7, 23-27 .10625422
[24] Ganot, P., Bortolin, M.L., and Kiss, T. (1997). Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs.
Cell 89, 799-809 .9182768
[25] Ghoshal, K., and Jacob, S.T. (1997). An alternative molecular mechanism of action of 5-fluorouracil, a potent anticancer drug.
Biochem Pharmacol 53, 1569-1575 .9264308
[26] Grosjean, H. (2009). Nucleic Acids are Not Boring Long Polymers of Only Four Types of Nucleotides: A Guided Tour
. In: DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution . Grosjean H. ed. Austin,
Texas:
Landes Bioscience. 1-18 .
[27] Grozdanov, P., and Meier, U.T. (2009). Multicomponent Machines in RNA Modification: H/ACA Ribonucleoproteins
. In: DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution . Grosjean H. ed. Austin,
Texas:
Landes Bioscience. 450-460 .
[28] Hausner, T.P., Giglio, L.M., and Weiner, A.M. (1990). Evidence for base-pairing between mammalian U2 and U6 small nuclear ribonucleoprotein particles.
Genes Dev 4, 2146-2156 .2176635
[29] Heidelberger, C., Chaudhuri, N.K., Danneberg, P., Mooren, D., Griesbach, L., Duschinsky, R., Schnitzer, R.J., Pleven, E., and Scheiner, J. (1957). Fluorinated pyrimidines, a new class of tumour-inhibitory compounds.
Nature 179, 663-666 .13418758
[30] Hilliker, A.K., Mefford, M.A., and Staley, J.P. (2007). U2 toggles iteratively between the stem IIa and stem IIc conformations to promote pre-mRNA splicing.
Genes Dev 21, 821-834 .17403782
[31] Hoang, C., Chen, J., Vizthum, C.A., Kandel, J.M., Hamilton, C.S., Mueller, E.G., and Ferré-D’Amaré, A.R. (2006). Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure.
Mol Cell 24, 535-545 .17188032
[32] Hoang, C., and Ferré-D’Amaré, A.R. (2001). Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.
Cell 107, 929-939 .11779468
[33] Hoang, C., and Ferre-D’Amare, A.R. (2004). Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold.
RNA 10, 1026-1033 .15208439
[34] Hotchkiss, R.D. (1948). The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography.
J Biol Chem 175, 315-332 .18873306
[35] Hüttenhofer, A., Brosius, J., and Bachellerie, J.P. (2002). RNomics: identification and function of small, non-messenger RNAs.
Curr Opin Chem Biol 6, 835-843 .12470739
[36] Hüttenhofer, A., Kiefmann, M., Meier-Ewert, S., O’Brien, J., Lehrach, H., Bachellerie, J.P., and Brosius, J. (2001). RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse.
EMBO J 20, 2943-2953 .11387227
[37] Jády, B.E., and Kiss, T. (2001). A small nucleolar guide RNA functions both in 2′-O-ribose methylation and pseudouridylation of the U5 spliceosomal RNA.
EMBO J 20, 541-551 .11157760
[38] Karijolich, J., Huang, C., and Yu, Y.T. (2009). Spliceosomal snRNA pseudouridylation
. In: DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution . Grosjean H. ed. Austin,
TX:
Landes Bioscience. 461-474 .
[39] Karijolich, J., and Yu, Y.T. (2008). pre-mRNA splicing
. In: Wiley Encyclopedia of Chemical Biology . Begley T.P. ed.
Hoboken:
John Wiley & Sons. 1-10 .
[40] Kaya, Y., Del Campo, M., Ofengand, J., and Malhotra, A. (2004). Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold.
J Biol Chem 279, 18107-18110 .14999002
[41] 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 .8674114
[42] Kolev, N.G., and Steitz, J.A. (2006). In vivo assembly of functional U7 snRNP requires RNA backbone flexibility within the Sm-binding site.
Nat Struct Mol Biol 13, 347-353 .16547514
[43] Konarska, M.M., and Sharp, P.A. (1986). Electrophoretic separation of complexes involved in the splicing of precursors to mRNAs.
Cell 46, 845-855 .2944598
[44] Lafontaine, D.L., and Tollervey, D. (1998). Birth of the snoRNPs: the evolution of the modification-guide snoRNAs.
Trends Biochem Sci 23, 383-388 .9810226
[45] Lesser, C.F., and Guthrie, C. (1993). Mutations in U6 snRNA that alter splice site specificity: implications for the active site.
Science 262, 1982-1988 .8266093
[46] Li, L., and Ye, K. (2006). Crystal structure of an H/ACA box ribonucleoprotein particle.
Nature 443, 302-307 .16943774
[47] Liang, B., Xue, S., Terns, R.M., Terns, M.P., and Li, H. (2007). Substrate RNA positioning in the archaeal H/ACA ribonucleoprotein complex
. Nat Struct Mol Biol . Dec 2. [Epub ahead of print]
[48] Liang, B., Zhou, J., Kahen, E., Terns, R.M., Terns, M.P., and Li, H. (2009). Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA.
Nat Struct Mol Biol 16, 740-746 .19478803
[49] Lin, Y., and Kielkopf, C.L. (2008). X-ray structures of U2 snRNA-branchpoint duplexes containing conserved pseudouridines.
Biochemistry 47, 5503-5514 .18435545
[50] Longley, D.B., Harkin, D.P., and Johnston, P.G. (2003). 5-fluorouracil: mechanisms of action and clinical strategies.
Nat Rev Cancer 3, 330-338 .12724731
[51] Lowe, T.M., and Eddy, S.R. (1999). A computational screen for methylation guide snoRNAs in yeast.
Science 283, 1168-1171 .10024243
[52] Ma, X., Yang, C., Alexandrov, A., Grayhack, E.J., Behm-Ansmant, I., and Yu, Y.T. (2005). Pseudouridylation of yeast U2 snRNA is catalyzed by either an RNA-guided or RNA-independent mechanism.
EMBO J 24, 2403-2413 .15962000
[53] Ma, X., Zhao, X., and Yu, Y.T. (2003). Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism.
EMBO J 22, 1889-1897 .12682021
[54] Maden, B.E., Corbett, M.E., Heeney, P.A., Pugh, K., and Ajuh, P.M. (1995). Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA.
Biochimie 77, 22-29 .7599273
[55] Madhani, H.D., and Guthrie, C. (1992). A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome.
Cell 71, 803-817 .1423631
[56] Manival, X., Charron, C., Fourmann, J.B., Godard, F., Charpentier, B., and Branlant, C. (2006). Crystal structure determination and site-directed mutagenesis of the Pyrococcus abyssi aCBF5-aNOP10 complex reveal crucial roles of the C-terminal domains of both proteins in H/ACA sRNP activity.
Nucleic Acids Res 34, 826-839 .16456033
[57] Massenet, S., Motorin, Y., Lafontaine, D.L., Hurt, E.C., Grosjean, H., and Branlant, C. (1999). Pseudouridine 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 .10022901
[58] Massenet, S., Mougin, A., and Branlant, C. (1998). Posttranscriptional modifications in the U small nuclear RNAs
. In: Modification and Editing of RNA . Grosjean H. ed. Washington,
DC:
ASM Press. 201-228 .
[59] McCleverty, C.J., Hornsby, M., Spraggon, G., and Kreusch, A. (2007). Crystal structure of human Pus10, a novel pseudouridine synthase.
J Mol Biol 373, 1243-1254 .17900615
[60] Meier, U.T., and Blobel, G. (1994). NAP57, a mammalian nucleolar protein with a putative homolog in yeast and bacteria.
J Cell Biol 127, 1505-1514 .7798307
[61] Mizutani, K., Machida, Y., Unzai, S., Park, S.Y., and Tame, J.R. (2004). Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli.
Biochemistry 43, 4454-4463 .15078091
[62] Mueller, E.G., and Ferre-D'Amare, A.R. (2009). Paeudouridine Formation, the Most Common Transglycosylation in RNA
. In: DNA and RNA Modification Enzymes:Structure, Mechanism, Function and Evolution . Grosjean H. ed. Austin,
TX:
Landes Bioscience. 363-376 .
[63] Newby, M.I., and Greenbaum, N.L. (2001). A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch-site architecture.
RNA 7, 833-845 .11424937
[64] Newby, M.I., and Greenbaum, N.L. (2002). Sculpting of the spliceosomal branch site recognition motif by a conserved pseudouridine.
Nat Struct Biol 9, 958-965 .12426583
[65] Newman, A., and Norman, C. (1991). Mutations in yeast U5 snRNA alter the specificity of 5′ splice-site cleavage.
Cell 65, 115-123 .2013092
[66] Newman, A.J., and Norman, C. (1992). U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites.
Cell 68, 743-754 .1739979
[67] Ni, J., Tien, A.L., and Fournier, M.J. (1997). Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA.
Cell 89, 565-573 .9160748
[68] Nilsen, T.W. (1994). RNA-RNA interactions in the spliceosome: unraveling the ties that bind.
Cell 78, 1-4 .7518355
[69] Parker, R., Siliciano, P.G., and Guthrie, C. (1987). Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA.
Cell 49, 229-239 .3552247
[70] Parker, W.B., and Cheng, Y.C. (1990). Metabolism and mechanism of action of 5-fluorouracil.
Pharmacol Ther 48, 381-395 .1707544
[71] Perriman, R.J., and Ares, M. Jr. (2007). Rearrangement of competing U2 RNA helices within the spliceosome promotes multiple steps in splicing.
Genes Dev 21, 811-820 .17403781
[72] Rashid, R., Liang, B., Baker, D.L., Youssef, O.A., He, Y., Phipps, K., Terns, R.M., Terns, M.P., and Li, H. (2006). Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita.
Mol Cell 21, 249-260 .16427014
[73] Reddy, R., and Busch, H. (1988). Small nuclear RNAs: RNA sequences, structure, and modifications
. In: Structure and function of major and minor small nuclear ribonucleoprotein particles . Birnsteil M.L. ed.
Heidelberg:
Sringer-Verlag Press. 1-37 .
[74] Roovers, M., Hale, C., Tricot, C., Terns, M.P., Terns, R.M., Grosjean, H., and Droogmans, L. (2006). Formation of the conserved pseudouridine at position 55 in archaeal tRNA.
Nucleic Acids Res 34, 4293-4301 .16920741
[75] Saikia, M., Dai, Q., Decatur, W.A., Fournier, M.J., Piccirilli, J.A., and Pan, T. (2006). A systematic, ligation-based approach to study RNA modifications.
RNA 12, 2025-2033 .16963711
[76] Sawa, H., and Abelson, J. (1992). Evidence for a base-pairing interaction between U6 small nuclear RNA and 5′ splice site during the splicing reaction in yeast.
Proc Natl Acad Sci U S A 89, 11269-11273 .1333604
[77] Schattner, P., Barberan-Soler, S., and Lowe, T.M. (2006). A computational screen for mammalian pseudouridylation guide H/ACA RNAs.
RNA 12, 15-25 .16373490
[78] Schattner, P., Decatur, W.A., Davis, C.A., Ares, M. Jr, Fournier, M.J., and Lowe, T.M. (2004). Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome.
Nucleic Acids Res 32, 4281-4296 .15306656
[79] Sivaraman, J., Iannuzzi, P., Cygler, M., and Matte, A. (2004). Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli.
J Mol Biol 335, 87-101 .14659742
[80] Sivaraman, J., Sauvé, V., Larocque, R., Stura, E.A., Schrag, J.D., Cygler, M., and Matte, A. (2002). Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP.
Nat Struct Biol 9, 353-358 .11953756
[81] Smith, C.M., and Steitz, J.A. (1997). Sno storm in the nucleolus: new roles for myriad small RNPs.
Cell 89, 669-672 .9182752
[82] Sontheimer, E.J., and Steitz, J.A. (1993). The U5 and U6 small nuclear RNAs as active site components of the spliceosome.
Science 262, 1989-1996 .8266094
[83] Staley, J.P., and Guthrie, C. (1998). Mechanical devices of the spliceosome: motors, clocks, springs, and things.
Cell 92, 315-326 .9476892
[84] Tycowski, K.T., Smith, C.M., Shu, M.D., and Steitz, J.A. (1996). A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus.
Proc Natl Acad Sci U S A 93, 14480-14485 .8962077
[85] Tycowski, K.T., You, Z.H., Graham, P.J., and Steitz, J.A. (1998). Modification of U6 spliceosomal RNA is guided by other small RNAs.
Mol Cell 2, 629-638 .9844635
[86] Valadkhan, S., and Manley, J.L. (2003). Characterization of the catalytic activity of U2 and U6 snRNAs.
RNA 9, 892-904 .12810922
[87] Wassarman, D.A., and Steitz, J.A. (1992). Interactions of small nuclear RNA’s with precursor messenger RNA during in vitro splicing.
Science 257, 1918-1925 .1411506
[88] Will, C.L., and Lührmann, R. (2011). Spliceosome structure and function.
Cold Spring Harb Perspect Biol 3, 3.21441581
[89] Wu, G., Xiao, M., Yang, C., and Yu, Y.T. (2011a). U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP.
EMBO J 30, 79-89 .21131909
[90] Wu, G., Yu, A.T., Kantartzis, A., and Yu, Y.T. (2011b). Functions and mechanisms of spliceosomal small nuclear RNA pseudouridylation.
WIREs RNA 2, 571-581 .
[91] Wu, J.A., and Manley, J.L. (1991). Base pairing between U2 and U6 snRNAs is necessary for splicing of a mammalian pre-mRNA.
Nature 352, 818-821 .1831878
[92] Wyatt, G.R. (1950). Occurrence of 5-methylcytosine in nucleic acids.
Nature 166, 237-238 .15439258
[93] Wyatt, J.R., Sontheimer, E.J., and Steitz, J.A. (1992). Site-specific cross-linking of mammalian U5 snRNP to the 5′ splice site before the first step of pre-mRNA splicing.
Genes Dev 6, 2542-2553 .1340469
[94] Yang, C., McPheeters, D.S., and Yu, Y.T. (2005). Psi35 in the branch site recognition region of U2 small nuclear RNA is important for pre-mRNA splicing in Saccharomyces cerevisiae.
J Biol Chem 280, 6655-6662 .15611063
[95] Yean, S.L., and Lin, R.J. (1991). U4 small nuclear RNA dissociates from a yeast spliceosome and does not participate in the subsequent splicing reaction.
Mol Cell Biol 11, 5571-5577 .1833635
[96] Yu, Y.T., Scharl, E.C., Smith, C.M., and Steitz, J.A. (1999). The growing world of small nuclear ribonucleoproteins
. In: The RNA World . Gesteland R.F., Cech T.R., and Atkins J.F. eds.
Cold Spring Harbor:
Cold Spring Harbor Laboratory Press. 487-524 .
[97] Yu, Y.T., Shu, M.D., and Steitz, J.A. (1998). Modifications of U2 snRNA are required for snRNP assembly and pre-mRNA splicing.
EMBO J 17, 5783-5795 .9755178
[98] Yu, Y.T., Terns, R.M., and Terns, M.P. (2005). Mechanisms and functions of RNA-guided RNA modification
. In: Topics in Current Genetics . Grosjean H. ed.
New York:
Springer-Verlag. 223-262 .
[99] Zebarjadian, Y., King, T., Fournier, M.J., Clarke, L., and Carbon, J. (1999). Point mutations in yeast CBF5 can abolish in vivo pseudouridylation of rRNA.
Mol Cell Biol 19, 7461-7472 .10523634
[100] Zhao, X., Li, Z.H., Terns, R.M., Terns, M.P., and Yu, Y.T. (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 .12515384
[101] Zhao, X., and Yu, Y.T. (2004a). Detection and quantitation of RNA base modifications.
RNA 10, 996-1002 .15146083
[102] Zhao, X., and Yu, Y.T. (2004b). Pseudouridines in and near the branch site recognition region of U2 snRNA are required for snRNP biogenesis and pre-mRNA splicing in Xenopus oocytes.
RNA 10, 681-690 .15037777
[103] Zhao, X., and Yu, Y.T. (2007). Incorporation of 5-fluorouracil into U2 snRNA blocks pseudouridylation and pre-mRNA splicing in vivo.
Nucleic Acids Res 35, 550-558 .17169984
[104] Zhuang, Y., and Weiner, A.M. (1986). A compensatory base change in U1 snRNA suppresses a 5′ splice site mutation.
Cell 46, 827-835 .3757028
[105] Zhuang, Y., and Weiner, A.M. (1989). A compensatory base change in human U2 snRNA can suppress a branch site mutation.
Genes Dev 3, 1545-1552 .2612904
PDF(622 KB)
)
AI Summary
