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Journal of Nucleic Acids
Volume 2012, Article ID 369058, 40 pages
http://dx.doi.org/10.1155/2012/369058
Review Article

Chemical Approaches for Structure and Function of RNA in Postgenomic Era

Departments of Pharmacology and Biochemistry, College of Medicine, Dong-A University, 3-1 Dong Dae Shin Dong, Seo Gu, Busan 602-714, Republic of Korea

Received 18 October 2010; Revised 21 June 2011; Accepted 5 July 2011

Academic Editor: Dmitry A. Stetsenko

Copyright © 2012 Tae Suk Ro-Choi and Yong Chun Choi. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. S. Dunin-Horkawicz, A. Czerwoniec, M. J. Gajda, M. Feder, H. Grosjean, and J. M. Bujnicki, “MODOMICS: a database of RNA modification pathways,” Nucleic Acids Research., vol. 34, pp. D145–D149, 2006. View at Google Scholar · View at Scopus
  2. T. A. Cooper, L. Wan, and G. Dreyfuss, “RNA and Disease,” Cell, vol. 136, no. 4, pp. 777–793, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  3. J. D. Watson and F. H. C. Crick, “Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid,” Nature, vol. 171, no. 4356, pp. 737–738, 1953. View at Publisher · View at Google Scholar · View at Scopus
  4. I. R. Lehman, M. J. Bessman, E. S. Simms, and A. Kornberg, “Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from Escherichia coli,” Journal of Biological Chemistry, vol. 233, no. 1, pp. 163–170, 1958. View at Google Scholar · View at Scopus
  5. M. J. Bessman, I. R. Lehman, E. S. Simms, and A. Kornberg, “Enzymatic synthesis of deoxyribonucleic acid. II. General properties of the reaction,” Journal of Biological Chemistry, vol. 233, no. 1, pp. 171–177, 1958. View at Google Scholar · View at Scopus
  6. M. Muramatsu and H. Busch, “Isolation, composition, and function of nucleoli of tumors and other tissues,” in Methods in Cancer Research, H. Busch, Ed., vol. 2, Chapter 9, pp. 303–359, Academic Press, New York, NY, USA, 1967. View at Google Scholar
  7. T. S. Ro-Choi and H. Busch, “Low-molecular-weight nuclear RNAs,” in The Cell Nucleus, H. Busch, Ed., chapter 5, Academic Press, New York, NY, USA, 1974. View at Google Scholar
  8. J. Sperling, M. Azubel, and R. Sperling, “Structure and function of the pre-mRNA splicing machine,” Structure, vol. 16, no. 11, pp. 1605–1615, 2008. View at Publisher · View at Google Scholar · View at PubMed
  9. K. Randerath and E. Randerath, “A tritium derivative method for base analysis of ribonucleotides and RNA,” Procedures in Nucleic Acid Research, vol. 2, pp. 796–828, 1971. View at Google Scholar
  10. J. A. Gerlt, “Mechanistic principles of enzyme-catalyzed cleavage of phosphodiester bonds,” in Nucleases, S. M. Linn, R. S. Lloy, and J. R. Roberts, Eds., chapter 1, Cold Spring Harbor Laboratory, New York, NY, USA, 1993. View at Google Scholar
  11. Y. Motorin, S. Muller, I. Behm-Ansmant, and C. Branlant, “Identification of modified residues in RNAs by reverse transcription-based methods,” Methods in Enzymology, vol. 425, pp. 21–53, 2007. View at Publisher · View at Google Scholar · View at PubMed
  12. T. S. Ro-Choi, Y. C. Choi, D. Henning, J. McCloskey, and H. Busch, “Nucleotide sequence of U2 ribonucleic acid. The sequence of the 5' terminal oligonucleotide,” Journal of Biological Chemistry, vol. 250, no. 10, pp. 3921–3928, 1975. View at Google Scholar
  13. L. Cartegni, J. Wang, Z. Zhu, M. Q. Zhang, and A. R. Krainer, “ESEfinder: a web resource to identify exonic splicing enhancers,” Nucleic Acids Research, vol. 31, no. 13, pp. 3568–3571, 2003. View at Publisher · View at Google Scholar
  14. J. Brachet, The Biological Role of Ribonucleic Acids, Weizman Memorial Lecture Series, The Netherlands Elsevier Publishing, 6th edition, 1960.
  15. C. Branlant, A. Krol, J. P. Ebel et al., “Nucleotide sequences of nuclear U1A RNAs from chicken, rat and man,” Nucleic Acids Research, vol. 8, no. 18, pp. 4143–4154, 1980. View at Publisher · View at Google Scholar
  16. T. S. Ro-Choi and D. Henning, “Sequence of 5' oligonucleotide of U1 RNA from Novikoff hepatoma cells,” Journal of Biological Chemistry, vol. 252, no. 11, pp. 3814–3820, 1977. View at Google Scholar
  17. C. Branlant, A. Krol, J. P. Ebel, E. Lazar, B. Haendler, and M. Jacob, “U2 RNA shares a structural domain with U1, U4, and U5 RNAs,” EMBO Journal, vol. 1, no. 10, pp. 1259–1263, 1982. View at Google Scholar
  18. H. Shibata, T. S. Ro Choi, R. Reddy, Y. C. Choi, D. Henning, and H. Bush, “The primary nucleotide sequence of nuclear U2 ribonucleic acid. The 5' terminal portion of the molecule,” Journal of Biological Chemistry, vol. 250, no. 10, pp. 3909–3920, 1975. View at Google Scholar
  19. D. Suh, H. Busch, and R. Reddy, “Isolation and characterization of a human U3 small nucleolar RNA gene,” Biochemical and Biophysical Research Communications, vol. 137, no. 3, pp. 1133–1140, 1986. View at Google Scholar
  20. K. A. Parker and J. A. Steitz, “Structural analysis of the human U3 ribonucleoprotein particle reveal a conserved sequence available for base pairing with pre-rRNA,” Molecular and Cellular Biology, vol. 7, no. 8, pp. 2899–2913, 1987. View at Google Scholar
  21. T. S. Ro-Choi, “Nucleolar snoRNA and ribosome production,” Molecules and Cells, vol. 7, no. 4, pp. 451–467, 1997. View at Google Scholar
  22. A. Krol, C. Branlant, E. Lazar, H. Gallinaro, and M. Jacob, “Primary and secondary structures of chicken, rat and man nuclear U4 RNAs. Homologies with U1 and U5 RNAs,” Nucleic Acids Research, vol. 9, no. 12, pp. 2699–2716, 1981. View at Google Scholar
  23. S. Liu, P. Li, O. Dybkov et al., “Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP,” Science, vol. 316, no. 5821, pp. 115–120, 2007. View at Publisher · View at Google Scholar · View at PubMed
  24. R. Reddy, D. Henning, and H. Busch, “The primary nucleotide sequence of U4 RNA,” Journal of Biological Chemistry, vol. 256, no. 7, pp. 3532–3538, 1981. View at Google Scholar
  25. A. Krol, H. Gallinaro, E. Lazar et al., “The nuclear 5S RNAs from chicken, rat and man. U5 RNAs are encoded by multiple genes,” Nucleic Acids Research, vol. 9, no. 4, pp. 769–787, 1981. View at Google Scholar
  26. R. Reddy and H. Busch, “U-snRNAs of nuclear RNPs,” in The Cell Nucleus, H. Busch, Ed., vol. 8, chapter 7, pp. 261–306, Academic Press, New York, NY, USA, 1981. View at Google Scholar
  27. G. R. Kunkel, R. L. Maser, J. P. Calvet, and T. Pederson, “U6 small nuclear RNA is transcribed by RNA polymerase III,” Proceedings of the National Academy of Sciences of the United States of America, vol. 83, no. 22, pp. 8575–8579, 1986. View at Google Scholar
  28. P. Epstein, R. Reddy, D. Henning, and H. Busch, “The nucleotide sequence of nuclear U6 (4.7 S) RNA,” Journal of Biological Chemistry, vol. 255, no. 18, pp. 8901–8906, 1980. View at Google Scholar
  29. K. L. Mowry and J. A. Steitz, “Identification of the human U7 snRNP as one of several factors involved in the 3' end maturation of histone premessenger RNA's,” Science, vol. 238, no. 4834, pp. 1682–1687, 1987. View at Google Scholar
  30. K. Tyc and J. A. Steitz, “U3, U8 and U13 comprise a new class of mammalian snRNPs localized in the cell nucleolus,” EMBO Journal, vol. 8, no. 10, pp. 3113–3119, 1989. View at Google Scholar
  31. T. S. Ro, M. Muramatsu, and H. Busch, “Labeling of RNA of isolated nucleoli with UTP-2-14C,” Biochemical and Biophysical Research Communications, vol. 14, no. 2, pp. 149–155, 1964. View at Google Scholar
  32. Y. C. Choi, K. Smetana, and H. Busch, “Studies on RNA isolated from nucleolar fractions of Novikoff hepatoma cells by sequential extractions with dilute and concentrated salt solutions,” Experimental Cell Research, vol. 53, no. 2-3, pp. 582–602, 1968. View at Google Scholar
  33. E. S. Maxwell and M. J. Fournier, “The small nucleolar RNAs,” Annual Review of Biochemistry, vol. 64, pp. 897–934, 1995. View at Google Scholar
  34. K. T. Tycowski, N.G. Kolev, N. K. Conrad, V. Fok, and J. A. Steitz, “The ever-growing world of small nuclear ribonucleoproteins,” in The RNA World, R. F. Gesteland, T. R. Cech, and J. F. Atkins, Eds., chapter 12, pp. 327–368, CSHL Press, 2006. View at Google Scholar
  35. C. L. Will and R. Lührmann, “Spliceosome structure and function,” in The RNA World, R. F. Gesteland, T. R. Cech, and J. F. Atkins, Eds., chapter 13, pp. 369–400, CSHL Press, 2006. View at Google Scholar
  36. T. S. Ro-Choi, R. Reddy, Y. C. Choi, N. B. Raj, and D. Henning, “Primary sequence of U1 nuclear RNA and unusual feature of 5’ end structure of LMWN RNA,” Proceedings Federation of American Societies for Experimental Biology, vol. 33, p. 1548, 1974. View at Google Scholar
  37. T. S. Ro-Choi, “Nuclear snRNA and nuclear function (discovery of 5' cap structures in RNA),” Critical Reviews in Eukaryotic Gene Expression, vol. 9, no. 2, pp. 107–158, 1999. View at Google Scholar
  38. T. S. Ro-Choi, Y. Moriyama, Y. C. Choi, and H. Busch, “Isolation and purification of a nuclear 4.5S ribonucleic acid of the Novikoff hepatoma,” Journal of Biological Chemistry, vol. 245, no. 8, pp. 1970–1977, 1970. View at Google Scholar
  39. S. M. el-Khatib, T. S. Ro-Choi, Y. C. Choi, and H. Busch, “Studies on nuclear 4.5 S ribonucleic acid III of Novikoff hepatoma ascites cells,” Journal of Biological Chemistry, vol. 245, no. 13, pp. 3416–3421, 1970. View at Google Scholar
  40. G. Dreyfuss, M. J. Matunis, S. Piñol-Roma, and C. G. Burd, “hnRNP proteins and the biogenesis of mRNA,” Annual Review of Biochemistry, vol. 62, pp. 289–321, 1993. View at Google Scholar
  41. J. C. Long and J. F. Caceres, “The SR protein family of splicing factors: master regulators of gene expression,” Biochemical Journal, vol. 417, no. 1, pp. 15–27, 2009. View at Publisher · View at Google Scholar · View at PubMed
  42. G. Dreyfuss, “Structure and function of nuclear and cytoplasmic ribonucleoprotein particles,” Annual Review of Cell Biology, vol. 2, pp. 459–498, 1986. View at Google Scholar
  43. W. M. LeStourgeon, S. F. Barnett, and S. J. Northington, “Tetramer of core proteins of 40S nuclear ribonucleoprotein particles assemble to package nascent transcripts into a repeating array of regular particles,” in The Eukaryotic Nucleus, P. R. Strauss and S. H. Willson, Eds., vol. 2, pp. 477–502, The Telford Press, NJ, USA, 1990. View at Google Scholar
  44. M. Zuker, “Computer prediction of RNA structure,” in Methods in Enzymology, vol. 180, chapter 20, pp. 262–288, 1989. View at Publisher · View at Google Scholar
  45. D. E. Draper, “Protein-RNA recognition,” Annual Review of Biochemistry, vol. 64, pp. 593–620, 1995. View at Google Scholar
  46. H.-J. Kim and K. Han, “Automated modeling of the RNA folding process,” Molecules and Cells, vol. 5, pp. 406–412, 1995. View at Google Scholar
  47. T. S. Ro-Choi and Y. C. Choi, “Thermodynamic analyses of the constitutive splicing pathway for ovomucoid pre-mRNA,” Molecules and Cells, vol. 27, no. 6, pp. 657–665, 2009. View at Publisher · View at Google Scholar · View at PubMed
  48. T. S. Ro-Choi and Y. C. Choi, “Structural elements of dynamic RNA strings,” Molecules and Cells, vol. 16, no. 2, pp. 201–210, 2003. View at Google Scholar
  49. T. S. Ro-Choi and Y. C. Choi, “A modeling study of Co-transcriptional metabolism of hnRNP using FMR1 Gene,” Molecules and Cells, vol. 23, no. 2, pp. 228–238, 2007. View at Google Scholar
  50. J. S. Mattick, “The functional genomics of noncoding RNA,” Science, vol. 309, no. 5740, pp. 1527–1528, 2005. View at Publisher · View at Google Scholar · View at PubMed
  51. J. M. Claverie, “Fewer genes, more noncoding RNA,” Science, vol. 309, no. 5740, pp. 1529–1530, 2005. View at Publisher · View at Google Scholar · View at PubMed
  52. U. A. Ørom, T. Derrien, M. Beringer et al., “Long noncoding RNAs with enhancer-like function in human cells,” Cell, vol. 143, no. 1, pp. 46–58, 2010. View at Publisher · View at Google Scholar · View at PubMed
  53. W. J. Steele, N. Okamura, and H. Busch, “Effects of thioacetamide on the composition and biosynthesis of nucleolar and nuclear ribonucleic acid in rat liver,” Journal of Biological Chemistry, vol. 240, pp. 1742–1749, 1965. View at Google Scholar
  54. R. W. Holley, G. A. Everett, J. T. Madison, and A. Zamir, “Nucleotide sequence in the yeast alanine transfer ribonucleic acid,” Journal of Biological Chemistry, vol. 240, pp. 2122–2128, 1965. View at Google Scholar
  55. R. de Wachter and W. Fiers, “Studies on the bacteriophage MS2. IV. The 3′-OH terminal undecanucleotide sequence of the viral RNA chain,” Journal of Molecular Biology, vol. 30, no. 3, pp. 507–518, 1967. View at Google Scholar
  56. M. Silberklang, A. M. Gillum, and U. L. RajBhandary, “[3] Use of in Vitro 32P labeling in the sequence analysis of nonradioactive tRNAs,” Methods in Enzymology, vol. 59, no. C, pp. 58–109, 1979. View at Publisher · View at Google Scholar
  57. W. Y. Li, R. Reddy, D. Henning, P. Epstein, and H. Busch, “Nucleotide sequence of 7 S RNA. Homology to Alu DNA and La 4.5 S RNA,” Journal of Biological Chemistry, vol. 257, no. 9, pp. 5136–5142, 1982. View at Google Scholar
  58. T. S. Ro-Choi, “U3 RNA cap structure, m32,2,7GpppAmpA(m)pApG, of Novikoff hepatoma cell,” Molecules and Cells, vol. 6, no. 4, pp. 436–443, 1996. View at Google Scholar
  59. P. Carninci and Y. Hayashizaki, “High-efficiency full-length cDNA cloning,” Methods in Enzymology, vol. 303, pp. 19–44, 1999. View at Publisher · View at Google Scholar
  60. D. A. Peattie, “Direct chemical method for sequencing RNA,” Proceedings of the National Academy of Sciences of the United States of America, vol. 76, no. 4, pp. 1760–1764, 1979. View at Google Scholar
  61. Y. Kuchino and S. Nishimura, “Enzymatic RNA sequencing,” Methods in Enzymology, vol. 180, pp. 154–163, 1989. View at Publisher · View at Google Scholar
  62. B. G. Barrel, “Fractionation and sequence analysis of radioactive nucleotides,” Procedures in Nucleic Acid Research, vol. 2, pp. 751–779, 1971. View at Google Scholar
  63. K. Randerath, R. C. Gupta, and E. Randerath, “[3H] and [32P] derivative methods for base composition and sequence analysis of RNA,” Methods in Enzymology, vol. 65, no. C, pp. 638–680, 1971. View at Publisher · View at Google Scholar
  64. Y. C. Choi and H. Busch, “Modified nucleotides in T1 RNase oligonucleotides of 18S ribosomal RNA of the Novikoff hepatoma,” Biochemistry, vol. 17, no. 13, pp. 2551–2560, 1978. View at Google Scholar
  65. International Human Genome Sequencing Consortium, “Initial sequencing and analysis of the human genome,” Nature, vol. 409, no. 6838, pp. 860–921, 2001. View at Google Scholar
  66. J. Craig Venter, M. D. Adams, E. W. Myers et al., “The sequence of the human genome,” Science, vol. 291, no. 5507, pp. 1304–1351, 2001. View at Publisher · View at Google Scholar · View at PubMed
  67. R. H. Waterston, K. Lindblad-Toh, E. Birney et al., “Initial sequencing and comparative analysis of the mouse genome,” Nature, vol. 420, no. 6915, pp. 520–562, 2002. View at Publisher · View at Google Scholar · View at PubMed
  68. G. S. Wang and T. A. Cooper, “Splicing in disease: disruption of the splicing code and the decoding machinery,” Nature Reviews Genetics, vol. 8, no. 10, pp. 749–761, 2007. View at Publisher · View at Google Scholar · View at PubMed
  69. K. J. Hertel, “Combinatorial control of exon recognition,” Journal of Biological Chemistry, vol. 283, no. 3, pp. 1211–1215, 2008. View at Publisher · View at Google Scholar · View at PubMed
  70. S. Hausmann, S. Zheng, M. Costanzo et al., “Genetic and biochemical analysis of yeast and human cap trimethylguanosine synthase: functional overlap of 2,2,7-trimethylguanosine caps, small nuclear ribonucleoprotein components, PRE-mRNA splicing factors, and RNA decay pathways,” Journal of Biological Chemistry, vol. 283, no. 46, pp. 31706–31718, 2008. View at Publisher · View at Google Scholar · View at PubMed
  71. P. Misra, C. Qi, S. Yu et al., “Interaction of PIMT with transcriptional coactivators CBP, p300, and PBP differential role in transcriptional regulation,” Journal of Biological Chemistry, vol. 277, no. 22, pp. 20011–20019, 2002. View at Publisher · View at Google Scholar · View at PubMed
  72. J. Mouaikel, U. Narayanan, C. Verheggen et al., “Interaction between the small-nuclear-RNA cap hypermethylase and the spinal muscular atrophy protein, survival of motor neuron,” EMBO Reports, vol. 4, no. 6, pp. 616–622, 2003. View at Publisher · View at Google Scholar · View at PubMed
  73. P. T. Gilham, “An addition reaction specific for uridine and guanosine nucleotides and its application to the modification of ribonuclease action,” Journal of the American Chemical Society, vol. 84, no. 4, pp. 687–688, 1962. View at Google Scholar
  74. R. Naylor, N. W. Y. Ho, and P. T. Gilham, “Selective chemical modifications of uridine and pseudouridine in polynucleotides and their effect on the specificities of ribonuclease and phosphodiesterases,” Journal of the American Chemical Society, vol. 87, no. 18, pp. 4209–4210, 1965. View at Google Scholar
  75. N. W. Y. Ho and P. T. Gilham, “Reaction of pseudouridine and inosine with N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide,” Biochemistry, vol. 10, no. 20, pp. 3651–3657, 1971. View at Google Scholar
  76. A. G. Saponara and M. D. Enger, “Occurrence of N2,N2,7-methylguanosine in minor RNA species of a mammalian cell line,” Nature, vol. 223, no. 5213, pp. 1365–1366, 1969. View at Publisher · View at Google Scholar
  77. T. S. Ro-Choi, R. Redy, D. Henning, T. Takano, C. W. Taylor, and H. Busch, “Nucleotide sequence of 4.5S Ribonucleic Acid I of Novikoff hepatoma cell nuclei,” Journal of Biological Chemistry, vol. 247, no. 10, pp. 3205–3222, 1972. View at Google Scholar
  78. S. Schwartz, N. Gal-Mark, N. Kfir, R. Oren, E. Kim, and G. Ast, “Alu exonization events reveal features required for precise recognition of exons by the splicing machinery,” PLoS Computational Biology, vol. 5, no. 3, Article ID e1000300, 2009. View at Publisher · View at Google Scholar · View at PubMed
  79. K. Nagai, C. Oubridge, A. Kuglstatter, E. Menichelli, C. Isel, and L. Jovine, “Structure, function and evolution of the signal recognition particle,” EMBO Journal, vol. 22, no. 14, pp. 3479–3485, 2003. View at Publisher · View at Google Scholar · View at PubMed
  80. A. W. Prestayko, M. Tonato, B. C. Lewis, and H. Busch, “Heterogeneity of nucleolar U3 ribonucleic acid of the Novikoff hepatoma,” Journal of Biological Chemistry, vol. 246, no. 1, pp. 182–187, 1971. View at Google Scholar
  81. E. Randerath, C. T. Yu, and K. Randerath, “Base analysis of ribopolynucleotides by chemical tritium labeling: a methodological study with model nucleosides and purified tRNA species,” Analytical Biochemistry, vol. 48, no. 1, pp. 172–198, 1972. View at Google Scholar
  82. R. Reddy, T. S. Ro-Choi, D. Henning, H. Shibata, Y. C. Choi, and H. Busch, “Modified nucleosides of nuclear and nucleolar low molecular weight ribonucleic acid,” Journal of Biological Chemistry, vol. 247, no. 22, pp. 7245–7250, 1972. View at Google Scholar
  83. C. M. Mauritzen, Y. C. Choi, and H. Busch, “Preparation of Macromolecules of Very High Specific Activity of Tumor cells,” in Methods in Cancer Research, H. Busch, Ed., vol. 6, pp. 253–282, Academic Press, New York, NY, USA, 1970. View at Google Scholar
  84. Y. C. Choi and T. S. Ro-Choi, “Basic characteristics of different classes of cellular RNAs; a directory,” in Cell Biology; A Comprehensive Treatise, L. Goldstein and D. Prescott, Eds., vol. 3, chapter 12, pp. 609–667, New York Academic, New York, NY, USA, 1980. View at Google Scholar
  85. H. Miyoshi, D. S. Dwyer, B. D. Keiper, M. Jankowska-Anyszka, E. Darzynkiewicz, and R. E. Rhoads, “Discrimination between mono- and trimethylated cap structures by two isoforms of Caenorhabditis elegans eIF4E,” EMBO Journal, vol. 21, no. 17, pp. 4680–4690, 2002. View at Publisher · View at Google Scholar
  86. C. Mazza, M. Ohno, A. Segref, I. W. Mattaj, and S. Cusack, “Crystal structure of the human nuclear cap binding complex,” Molecular Cell, vol. 8, no. 2, pp. 383–396, 2001. View at Publisher · View at Google Scholar
  87. C. Mazza, A. Segref, I. W. Mattaj, and S. Cusack, “Large-scale induced fit recognition of an m7GpppG cap analogue by the human nuclear cap-binding complex,” EMBO Journal, vol. 21, no. 20, pp. 5548–5557, 2002. View at Publisher · View at Google Scholar
  88. C. M. Smith and J. A. Steitz, “Sno storm in the nucleolus: new roles for myriad small RNPs,” Cell, vol. 89, no. 5, pp. 669–672, 1997. View at Google Scholar
  89. C. Y. Lee, A. Lee, and G. Chanfreau, “The roles of endonucleolytic cleavage and exonucleolytic digestion in the 5′-end processing of S. cerevisiae box C/D snoRNAs,” RNA, vol. 9, no. 11, pp. 1362–1370, 2003. View at Publisher · View at Google Scholar
  90. T. Monecke, A. Dickmanns, and R. Ficner, “Structural basis for m7G-cap hypermethylation of small nuclear, small nucleolar and telomerase RNA by the dimethyltransferase TGS1,” Nucleic Acids Research, vol. 37, no. 12, pp. 3865–3877, 2009. View at Publisher · View at Google Scholar · View at PubMed
  91. A. Strasser, A. Dickmanns, R. Lührmann, and R. Ficner, “Structural basis for m3G-cap-mediated nuclear import of spliceosomal UsnRNPs by snurportin1,” EMBO Journal, vol. 24, no. 13, pp. 2235–2243, 2005. View at Publisher · View at Google Scholar · View at PubMed
  92. J. L. Chen, M. A. Blasco, and C. W. Greider, “Secondary structure of vertebrate telomerase RNA,” Cell, vol. 100, no. 5, pp. 503–514, 2000. View at Google Scholar
  93. J. Franke, J. Gehlen, and A. E. Ehrenhofer-Murray, “Hypermethylation of yeast telomerase RNA by the snRNA and snoRNA methyltransferase Tgs1,” Journal of Cell Science, vol. 121, no. 21, pp. 3553–3560, 2008. View at Publisher · View at Google Scholar · View at PubMed
  94. B. E. Jády, E. Bertrand, and T. Kiss, “Human telomerase RNA and box H/ACA scaRNAs share a common Cajal body-specific localization signal,” Journal of Cell Biology, vol. 164, no. 5, pp. 647–652, 2004. View at Publisher · View at Google Scholar · View at PubMed
  95. S. Bektesh, K. Van Doren, and D. Hirsh, “Presence of the Caenorhabditis elegans spliced leader on different mRNAs and in different genera of nematodes,” Genes & Development, vol. 2, no. 10, pp. 1277–1283, 1988. View at Google Scholar
  96. T. Blumenthal, “Trans-splicing and operons,” WormBook, pp. 1–9, 2005. View at Publisher · View at Google Scholar · View at PubMed
  97. C. K. Ho and S. Shuman, “Distinct roles for CTD Ser-2 and Ser-5 phosphorylation in the recruitment and allosteric activation of mammalian mRNA capping enzyme,” Molecular Cell, vol. 3, no. 3, pp. 405–411, 1999. View at Publisher · View at Google Scholar
  98. K. Mizumoto and Y. Kaziro, “Messenger RNA capping enzymes from eukaryotic cells,” Progress in Nucleic Acid Research and Molecular Biology, vol. 34, no. C, pp. 1–28, 1987. View at Publisher · View at Google Scholar
  99. D. Testa and A. K. Banerjee, “Two methyltransferase activities in the purified virions of vesicular stomatitis virus,” Journal of Virology, vol. 24, no. 3, pp. 786–793, 1977. View at Google Scholar
  100. A. J. Shatkin, “Capping of eucaryotic mRNAs,” Cell, vol. 9, no. 4, pp. 645–653, 1976. View at Google Scholar
  101. S. R. Langberg and B. Moss, “Post-transcriptional modifications of mRNA. Purification and characterization of cap I and cap II RNA (nucleoside-2'-)-methyltransferases from HeLa cells,” Journal of Biological Chemistry, vol. 256, no. 19, pp. 10054–10060, 1981. View at Google Scholar
  102. D. L. Spector, “Colocalization of U1 and U2 small nuclear RNPs by immunocytochemistry,” Biology of the Cell, vol. 51, no. 1, pp. 109–112, 1984. View at Google Scholar
  103. G. Plessel, U. Fischer, and R. Luhrmann, “m3G cap hypermethylation of U1 small nuclear ribonucleoprotein (snRNP) in vitro: evidence that the U1 small nuclear RNA-(guanosine-N2)- methyltransferase is a non-snRNP cytoplasmic protein that requires a binding site on the Sm core domain,” Molecular and Cellular Biology, vol. 14, no. 6, pp. 4160–4172, 1994. View at Google Scholar
  104. I. W. Mattaj, “Cap trimethylation of U snRNA is cytoplasmic and dependent on U snRNP protein binding,” Cell, vol. 46, no. 6, pp. 905–911, 1986. View at Google Scholar
  105. C. Verheggen, D. L. J. Lafontaine, D. Samarsky et al., “Mammalian and yeast U3 snoRNPs are matured in specific and related nuclear compartments,” EMBO Journal, vol. 21, no. 11, pp. 2736–2745, 2002. View at Publisher · View at Google Scholar · View at PubMed
  106. J. Mouaikel, C. Verheggen, E. Bertrand, J. Tazi, and R. Bordonné, “Hypermethylation of the cap structure of both yeast snRNAs and snoRNAs requires a conserved methyltransferase that is localized to the nucleolus,” Molecular Cell, vol. 9, no. 4, pp. 891–901, 2002. View at Publisher · View at Google Scholar
  107. S. J. Baserga, M. Gilmore-Hebert, and X. W. Yang, “Distinct molecular signals for nuclear import of the nucleolar snRNA, U3,” Genes and Development, vol. 6, no. 6, pp. 1120–1130, 1992. View at Google Scholar
  108. M. P. Terns and J. E. Dahlberg, “Retention and 5' cap trimethylation of U3 snRNA in the nucleus,” Science, vol. 264, no. 5161, pp. 959–961, 1994. View at Google Scholar
  109. Y. Zhu, C. Qi, W. Q. Cao, A. V. Yeldandi, M. S. Rao, and J. K. Reddy, “Cloning and characterization of PIMT, a protein with a methyltransferase domain, which interacts with and enhances nuclear receptor coactivator PRIP function,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 18, pp. 10380–10385, 2001. View at Publisher · View at Google Scholar · View at PubMed
  110. C. Girard, C. Verheggen, H. Neel et al., “Characterization of a short isoform of human Tgs1 hypermethylase associating with small nucleolar ribonucleoprotein core proteins and produced by limited proteolytic processing,” Journal of Biological Chemistry, vol. 283, no. 4, pp. 2060–2069, 2008. View at Publisher · View at Google Scholar · View at PubMed
  111. O. Komonyi, G. Pápai, I. Enunlu et al., “DTL, the Drosophila homolog of PIMT/Tgs1 nuclear receptor coactivator-interacting protein/RNA methyltransferase, has an essential role in development,” Journal of Biological Chemistry, vol. 280, no. 13, pp. 12397–12404, 2005. View at Publisher · View at Google Scholar · View at PubMed
  112. S. Hausmann and S. Shuman, “Specificity and mechanism of RNA cap guanine-N2 methyltransferase (Tgs1),” Journal of Biological Chemistry, vol. 280, no. 6, pp. 4021–4024, 2005. View at Publisher · View at Google Scholar · View at PubMed
  113. S. Hausmann and S. Shuman, “Giardia lamblia RNA cap guanine-N2 methyltransferase (Tgs2),” Journal of Biological Chemistry, vol. 280, no. 37, pp. 32101–32106, 2005. View at Publisher · View at Google Scholar · View at PubMed
  114. J. D. Bangs, P. F. Crain, T. Hashizume, J. A. McCloskey, and J. C. Boothroyd, “Mass spectrometry of mRNA cap 4 from trypanosomatids reveals two novel nucleosides,” Journal of Biological Chemistry, vol. 267, no. 14, pp. 9805–9815, 1992. View at Google Scholar
  115. B. Mittra, J. R. Zamudio, J. M. Bujnicki et al., “The TbMTr1 spliced leader RNA cap 1 2′-O-ribose methyltransferase from Trypanosoma brucei acts with substrate specificity,” Journal of Biological Chemistry, vol. 283, no. 6, pp. 3161–3172, 2008. View at Publisher · View at Google Scholar · View at PubMed
  116. Y. Takagi, S. Sindkar, D. Ekonomidis, M. P. Hall, and C. K. Ho, “Trypanosoma brucei encodes a bifunctional capping enzyme essential for cap 4 formation on the spliced leader RNA,” Journal of Biological Chemistry, vol. 282, no. 22, pp. 15995–16005, 2007. View at Publisher · View at Google Scholar · View at PubMed
  117. M. P. Hall and C. Kiong Ho, “Characterization of a Trypanosoma brucei RNA cap (guanine N-7) methyltransferase,” RNA, vol. 12, no. 3, pp. 488–497, 2006. View at Publisher · View at Google Scholar · View at PubMed
  118. E. Silva, E. Ullu, R. Kobayashi, and C. Tschudi, “Trypanosome capping enzymes display a novel two-domain structure,” Molecular and Cellular Biology, vol. 18, no. 8, pp. 4612–4619, 1998. View at Google Scholar
  119. J. A. McCloskey, “Constituents of nucleic acids: overview and strategy,” Methods in Enzymology, vol. 193, pp. 771–790, 1990. View at Google Scholar · View at Scopus
  120. R. J. Taft, K. C. Pang, T. R. Mercer, M. Dinger, and J. S. Mattick, “Non-coding RNAs: regulators of disease,” Journal of Pathology, vol. 220, no. 2, pp. 126–139, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus