Multiplicity of 5′ cap structures present on short RNAs

PLoS ONE

Volumn 9, Issue 7, 2014, Pages

  Abdelhamid, Rehab F ^a   Plessy, Charles ^a   Yamauchi, Yoshio ^b   Taoka, Masato ^b   De Hoon, Michiel ^a   Gingeras, Thomas R ^c   Isobe, Toshiaki ^b   Carninci, Piero ^a  

^a RIKEN   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

7 METHYLGUANOSINE; PYROPHOSPHATE; RNA; SHORT RNA; SMALL NUCLEOLAR RNA; UNCLASSIFIED DRUG; CAPPED RNA;

ARTICLE; BIOTYPE; CHEMICAL MODIFICATION; CONTROLLED STUDY; DNA LIBRARY; IMMUNOPRECIPITATION; MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE; RNA CAPPING; RNA PROCESSING; THIN LAYER CHROMATOGRAPHY; CONFORMATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY;

CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CHROMATOGRAPHY, THIN LAYER; MASS SPECTROMETRY; NUCLEIC ACID CONFORMATION; RNA CAPS;

EID: 84905394878     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0102895     Document Type: Article

References (52)

1. Shimotohno K, Kodama Y, Hashimoto J, Miura KI (1977) Importance of 5′-terminal blocking structure to stabilize mRNA in eukaryotic protein synthesis. Proc Natl Acad Sci U S A 74: 2734-2738. (Pubitemid 8150810)
2. Banerjee AK (1980) 5′-terminal cap structure in eucaryotic messenger ribonucleic acids. Microbiol Mol Biol Rev 44: 175-205.
3. Matera AG, Terns RM, Terns MP (2007) Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol 8: 209-220.
4. Singh R, Reddy R (1989) Gamma-monomethyl phosphate: a cap structure in spliceosomal U6 small nuclear RNA. Proc Natl Acad Sci U S A 86: 8280-8283. (Pubitemid 19286043)
5. O'Mullane L, Eperon IC (1998) The Pre-mRNA 5′ Cap Determines Whether U6 Small Nuclear RNA Succeeds U1 Small Nuclear Ribonucleoprotein Particle at 5′ Splice Sites. Mol Cell Biol 18: 7510-7520. (Pubitemid 28533069)
6. Hsuchen C-C, Dubin DT (1976) Di- and trimethylated congeners of 7-methylguanine in Sindbis virus mRNA. Nature 264: 190-191.
7. Benarroch D, Jankowska-Anyszka M, Stepinski J, Darzynkiewicz E, Shuman S (2010) Cap Analog Substrates Reveal Three Clades of Cap Guanine-N2 Methyltransferases with Distinct Methyl Acceptor Specificities. RNA 16: 211-220.
8. Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, et al. (2008) Hidden layers of human small RNAs. BMC Genomics 9: 157.
9. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, et al. (2005) The Transcriptional Landscape of the Mammalian Genome. Science 309: 1559-1563.
10. Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, et al. (2004) Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. PLoS Biol 2: e162.
11. Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, et al. (2012) The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res 41: D64-D69.
12. Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P, et al. (2009) Small RNAs Derived from snoRNAs. RNA 15: 1233-1240.
13. Lee YS, Shibata Y, Malhotra A, Dutta A (2009) A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 23: 2639-2649.
14. Fejes-Toth K, Sotirova V, Sachidanandam R, Assaf G, Hannon GJ, et al. (2009) Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457: 1028-1032.
15. Kapranov P, Ozsolak F, Kim SW, Foissac S, Lipson D, et al. (2010) New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism. Nature 466: 642-646.
16. McCue AD, Slotkin RK (2012) Transposable element small RNAs as regulators of gene expression. Trends Genet. 28(12): 616-623.
17. Qureshi IA, Mehler MF (2012) Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat Rev Neurosci 13: 528-541.
18. Mazières J, Catherinne C, Delfour O, Gouin S, Rouquette I, et al. (2013) Alternative Processing of the U2 Small Nuclear RNA Produces a 19-22nt Fragment with Relevance for the Detection of Non-Small Cell Lung Cancer in Human Serum. PLoS ONE 8: e60134.
19. Otsuka Y, Kedersha NL, Schoenberg DR (2009) Identification of a cytoplasmic complex that adds a cap onto 5′-monophosphate RNA. Mol Cell Biol 29: 2155-2167.
20. Ro-Choi TS (1999) Nuclear snRNA and nuclear function (discovery of 5′ cap structures in RNA). Crit Rev Eukaryot Gene Expr 9: 107-158.
21. Ro-Choi TS, Choi YC (2012) Chemical Approaches for Structure and Function of RNA in Postgenomic Era. J Nucleic Acids 2012: 369058.
22. Takahashi H, Kato S, Murata M, Carninci P (2012) CAGE (Cap Analysis of Gene Expression): A Protocol for the Detection of Promoter and Transcriptional Networks. In: Deplancke B, Gheldof N, editors. Gene Regulatory Networks. Totowa, NJ: Humana Press, Vol. 786. 181-200.
23. Kawano M, Kawazu C, Lizio M, Kawaji H, Carninci P, et al. (2010) Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing. BioTechniques 49: 751-755.
24. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
25. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
26. Ruan J, Ullu E, Tschudi C (2007) Characterization of the Trypanosoma brucei cap hypermethylase Tgs1. Mol Biochem Parasitol 155: 66-69. (Pubitemid 47042216)
27. Girard C, Verheggen C, Neel H, Cammas A, Vagner S, et al. (2008) Characterization of a Short Isoform of Human Tgs1 Hypermethylase Associating with Small Nucleolar Ribonucleoprotein Core Proteins and Produced by Limited Proteolytic Processing. J Biol Chem 283: 2060-2069.
28. Krainer AR (1988) Pre-mRNA splicing by complementation with purified human UI, U2, U4/U6 and U5 snRNPs. Nucleic Acids Res 16: 9415-9429.
29. Hartmann RK, Bindereif A, Schon A, Westhof E (2009) Handbook of RNA biochemistry student edition. Weinheim: Wiley-VCH-Verl.pp133-150.
30. Bochner BR, Ames BN (1982) Complete analysis of cellular nucleotides by two-dimensional thin layer chromatography. J Biol Chem 257: 9759-9769. (Pubitemid 13205141)
31. Simoes-Barbosa A, Louly C, Franco OL, Rubio MA, Alfonzo JD, et al. (2008) The Divergent Eukaryote Trichomonas Vaginalis Has an m7G Cap Methyltransferase Capable of a Single N2 Methylation. Nucleic Acids Res 36: 6848-6858.
32. Grosjean H, Droogmans L, Roovers M, Keith G (2007) Detection of Enzymatic Activity of Transfer RNA Modification Enzymes Using Radiolabeled tRNA Substrates. In: Jonatha M Gott, editor. Methods in Enzymology. Academic Press, Vol. Volume 425. 55-101.
33. Keith G (1995) Mobilities of modified ribonucleotides on two-dimensional cellulose thin-layer chromatography. Biochimie 77: 142-144.
34. Limbach PA, Crain PF, Pomerantz SC, McCloskey JA (1995) structures of posttranscriptional modified nucleosides from RNA. Biochimie 77: 135-138.
35. Huang F, Yarus M (1997) 5′-RNA Self-Capping from Guanosine Diphosphate. Biochemistry (Mosc) 36: 6557-6563.
36. Lerner MR, Boyle JA, Mount SM, Wolin SL, Steitz JA (1980) Are snRNPs involved in splicing? Nature 283: 220-224. (Pubitemid 10171146)
37. Perry KL, Watkins KP, Agabian N (1987) Trypanosome mRNAs have unusual "cap 4" structures acquired by addition of a spliced leader. Proc Natl Acad Sci U S A 84: 8190-8194. (Pubitemid 18033443)
38. Camper SA, Albers RJ, Coward JK, Rottman FM (1984) Effect of undermethylation on mRNA cytoplasmic appearance and half-life. Mol Cell Biol 4: 538-543.
39. Dimock K, Stoltzfus CM (1979) Processing and function of undermethylated chicken embryo fibroblast mRNA. J Biol Chem 254: 5591-5594.
40. Zaitseva L, Myers R, Fassati A (2006) tRNAs Promote Nuclear Import of HIV-1 Intracellular Reverse Transcription Complexes. PLoS Biol 4: e332.
41. Simos G, Hurt E (1999) Transfer RNA biogenesis: A visa to leave the nucleus. Curr Biol 9: R238-R241. (Pubitemid 29194866)
42. Arts G-J, Fornerod M, Mattaj lain W (1998) Identification of a nuclear export receptor for tRNA. Curr Biol 8: 305-314. (Pubitemid 28159116)
43. Hanada T, Weitzer S, Mair B, Bernreuther C, Wainger BJ, et al. (2013) CLP1 links tRNA metabolism to progressive motor-neuron loss. Nature 495: 474-480.
44. Iwanami Y, Brown GM (1968) Methylated bases of ribosomal ribonucleic acid from HeLa cells. Arch Biochem Biophys 126: 8-15.
45. Rozenski J, Crain PF, McCloskey JA (1999) The RNA Modification Database: 1999 update. Nucleic Acids Res 27: 196-197. doi:10.1093/nar/27.1.196. (Pubitemid 29209437)
46. Lipkin D, Talbert PT, Cohn M (1954) The Mechanism of the Alkaline Hydrolysis of Ribonucleic Acids. J Am Chem Soc 76: 2871-2872.
47. Helm M, Florentz C, Chomyn A, Attardi G (1999) Search for Differences in Post-Transcriptional Modification Patterns of Mitochondrial DNA-Encoded Wild-Type and Mutant Human tRNALys and tRNALeu(UUR). Nucleic Acids Res 27: 756-763. (Pubitemid 29209362)
48. Helm M (2006) Post-transcriptional nucleotide modification and alternative folding of RNA. Nucleic Acids Res 34: 721-733.
49. Hausmann S, Zheng S, Costanzo M, Brost RL, Garcin D, et al. (2008) Genetic and Biochemical Analysis of Yeast and Human Cap Trimethylguanosine Synthase. Functional Overlap of 2,2,7- Trimethyguanosine Caps, Small Nuclear Ribonucleoprotein Components, Pre-mRNA Splicing Factors, and RNA Decay Pathways. J Biol Chem 283: 31706-31718.
50. Hausmann S, Shuman S (2005) Giardia Lamblia RNA Cap Guanine-N2 Methyltransferase (Tgs2). J Biol Chem 280: 32101-32106. (Pubitemid 41361815)
51. Kuge H, Brownlee GG, Gershon PD, Richter JD (1998) Cap ribose methylation of c-mos mRNA stimulates translation and oocyte maturation in Xenopus laevis. Nucleic Acids Res 26: 3208-3214. (Pubitemid 28288920)
52. Zuberek J, Wyslouch-Cieszynska A, Niedzwiecka A, Dadlez M, Stepinski J, et al. (2003) Phosphorylation of eIF4E attenuates its interaction with mRNA 5′ cap analogs by electrostatic repulsion: Intein-mediated protein ligation strategy to obtain phosphorylated protein. RNA 9: 52-61. (Pubitemid 36206302)