-
2
-
-
58149191269
-
MODOMICS: A database of RNA modification pathways. 2008 update
-
Czerwoniec, A. et al. MODOMICS: a database of modification pathways. 2008 update. Nucleic Acids Res. 37, D118-D121 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Czerwoniec, A.1
-
3
-
-
0344223281
-
Transfer RNA modification: Influence on translational frameshifting and metabolism
-
Bjork, G.R. et al. Transfer RNA modification: influence on translational frameshifting and metabolism. FEBS Lett. 452, 47-51 (1999).
-
(1999)
FEBS Lett.
, vol.452
, pp. 47-51
-
-
Bjork, G.R.1
-
4
-
-
0035801515
-
Improvement of reading frame maintenance is a common function for several tRNA modifications
-
Urbonavicius, J. et al. Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J. 20, 4863-4873 (2001).
-
(2001)
EMBO J.
, vol.20
, pp. 4863-4873
-
-
Urbonavicius, J.1
-
5
-
-
0037053384
-
Accurate translation of the genetic code depends on tRNA modified nucleosides
-
Yarian, C. et al. Accurate translation of the genetic code depends on tRNA modified nucleosides. J. Biol. Chem. 277, 16391-16395 (2002).
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 16391-16395
-
-
Yarian, C.1
-
6
-
-
33846269602
-
TRNA's wobble decoding of the genome: 40 years of modification
-
Agris, P.F., Vendeix, F.A. & Graham, W.D. tRNA's wobble decoding of the genome: 40 years of modification. J. Mol. Biol. 366, 1-13 (2007).
-
(2007)
J. Mol. Biol.
, vol.366
, pp. 1-13
-
-
Agris, P.F.1
Vendeix, F.A.2
Graham, W.D.3
-
7
-
-
77953656943
-
TRNA stabilization by modified nucleotides
-
Motorin, Y. & Helm, M. tRNA stabilization by modified nucleotides. Biochemistry 49, 4934-4944 (2010).
-
(2010)
Biochemistry
, vol.49
, pp. 4934-4944
-
-
Motorin, Y.1
Helm, M.2
-
8
-
-
29544450711
-
Rapid tRNA decay can result from lack of non-essential modifications
-
Alexandrov, A. et al. Rapid tRNA decay can result from lack of non-essential modifications. Mol. Cell 21, 87-96 (2006).
-
(2006)
Mol. Cell
, vol.21
, pp. 87-96
-
-
Alexandrov, A.1
-
9
-
-
67650604265
-
Stressing out over tRNA cleavage
-
Thompson, D.M. & Parker, R. Stressing out over tRNA cleavage. Cell 138, 215-219 (2009).
-
(2009)
Cell
, vol.138
, pp. 215-219
-
-
Thompson, D.M.1
Parker, R.2
-
10
-
-
36749085941
-
Trm9-catalyzed tRNA modifications link translation to the DNA damage response
-
Begley, U. et al. Trm9-catalyzed tRNA modifications link translation to the DNA damage response. Mol. Cell 28, 860-870 (2007).
-
(2007)
Mol. Cell
, vol.28
, pp. 860-870
-
-
Begley, U.1
-
11
-
-
70849104780
-
Innate immune and chemically triggered oxidative stress modifies translational fidelity
-
Netzer, N. et al. Innate immune and chemically triggered oxidative stress modifies translational fidelity. Nature 462, 522-526 (2009).
-
(2009)
Nature
, vol.462
, pp. 522-526
-
-
Netzer, N.1
-
12
-
-
0026727639
-
Thiolation of transfer RNA in Escherichia coli varies with growth rate
-
Emilsson, V., Naslund, A.K. & Kurland, C.G. Thiolation of transfer RNA in Escherichia coli varies with growth rate. Nucleic Acids Res. 20, 4499-4505 (1992).
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 4499-4505
-
-
Emilsson, V.1
Naslund, A.K.2
Kurland, C.G.3
-
13
-
-
84861671920
-
Translational control of cell division by Elongator
-
Bauer, F. et al. Translational control of cell division by Elongator. Cell Rep. 1, 424-433 (2012).
-
(2012)
Cell Rep.
, vol.1
, pp. 424-433
-
-
Bauer, F.1
-
14
-
-
84864828979
-
Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins
-
Chan, C.T. et al. Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat. Commun. 3, 937 (2012).
-
(2012)
Nat. Commun.
, vol.3
, pp. 937
-
-
Chan, C.T.1
-
15
-
-
78650683942
-
A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress
-
Chan, C.T. et al. A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genet. 6, e1001247 (2010).
-
(2010)
PLoS Genet.
, vol.6
-
-
Chan, C.T.1
-
16
-
-
34548801413
-
Detection of enzymatic activity of transfer RNA modification enzymes using radiolabeled tRNA substrates
-
Grosjean, H., Droogmans, L., Roovers, M. & Keith, G. Detection of enzymatic activity of transfer RNA modification enzymes using radiolabeled tRNA substrates. Methods Enzymol. 425, 55-101 (2007).
-
(2007)
Methods Enzymol.
, vol.425
, pp. 55-101
-
-
Grosjean, H.1
Droogmans, L.2
Roovers, M.3
Keith, G.4
-
17
-
-
38649140699
-
The many applications of acid urea polyacrylamide gel electrophoresis to studies of tRNAs and aminoacyl-tRNA synthetases
-
Köhrer, C. & Rajbhandary, U.L. The many applications of acid urea polyacrylamide gel electrophoresis to studies of tRNAs and aminoacyl-tRNA synthetases. Methods 44, 129-138 (2008).
-
(2008)
Methods
, vol.44
, pp. 129-138
-
-
Köhrer, C.1
Rajbhandary, U.L.2
-
18
-
-
34548789633
-
Mass spectrometric identification and characterization of RNA-modifying enzymes
-
Suzuki, T., Ikeuchi, Y., Noma, A. & Sakaguchi, Y. Mass spectrometric identification and characterization of RNA-modifying enzymes. Methods Enzymol. 425, 211-229 (2007).
-
(2007)
Methods Enzymol.
, vol.425
, pp. 211-229
-
-
Suzuki, T.1
Ikeuchi, Y.2
Noma, A.3
Sakaguchi, Y.4
-
19
-
-
33745938634
-
Mass spectrometry of RNA: Linking the genome to the proteome
-
Meng, Z. & Limbach, P.A. Mass spectrometry of RNA: linking the genome to the proteome. Brief. Funct. Genomic Proteomic 5, 87-95 (2006).
-
(2006)
Brief. Funct. Genomic Proteomic
, vol.5
, pp. 87-95
-
-
Meng, Z.1
Limbach, P.A.2
-
20
-
-
0025612935
-
Analysis of RNA hydrolyzates by liquid chromatography-mass spectrometry
-
Pomerantz, S.C. & McCloskey, J.A. Analysis of RNA hydrolyzates by liquid chromatography-mass spectrometry. Methods Enzymol. 193, 796-824 (1990).
-
(1990)
Methods Enzymol.
, vol.193
, pp. 796-824
-
-
Pomerantz, S.C.1
McCloskey, J.A.2
-
21
-
-
0028322189
-
Summary: The modified nucleosides of RNA
-
Limbach, P.A., Crain, P.F. & McCloskey, J.A. Summary: the modified nucleosides of RNA. Nucleic Acids Res. 22, 2183-2196 (1994).
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 2183-2196
-
-
Limbach, P.A.1
Crain, P.F.2
McCloskey, J.A.3
-
22
-
-
0032918555
-
The RNA Modification Database: 1999 update
-
Rozenski, J., Crain, P.F. & McCloskey, J.A. The RNA Modification Database: 1999 update. Nucleic Acids Res. 27, 196-197 (1999).
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 196-197
-
-
Rozenski, J.1
Crain, P.F.2
McCloskey, J.A.3
-
23
-
-
77649263055
-
Agmatidine, a modified cytidine in the anticodon of archaeal tRNAIle, base pairs with adenosine but not with guanosine
-
Mandal, D. et al. Agmatidine, a modified cytidine in the anticodon of archaeal tRNAIle, base pairs with adenosine but not with guanosine. Proc. Natl. Acad. Sci. USA 107, 2872-2877 (2010).
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 2872-2877
-
-
Mandal, D.1
-
24
-
-
77949820848
-
Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea
-
Ikeuchi, Y. et al. Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Nat. Chem. Biol. 6, 277-282 (2010).
-
(2010)
Nat. Chem. Biol.
, vol.6
, pp. 277-282
-
-
Ikeuchi, Y.1
-
25
-
-
71549173705
-
Discovery and characterization of tRNAIle lysidine synthetase (TilS)
-
Suzuki, T. & Miyauchi, K. Discovery and characterization of tRNAIle lysidine synthetase (TilS). FEBS Lett. 584, 272-277 (2010).
-
(2010)
FEBS Lett.
, vol.584
, pp. 272-277
-
-
Suzuki, T.1
Miyauchi, K.2
-
26
-
-
84872686832
-
A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification
-
Miyauchi, K., Kimura, S. & Suzuki, T. A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. Nat. Chem. Biol. 9, 105-111 (2012).
-
(2012)
Nat. Chem. Biol.
, vol.9
, pp. 105-111
-
-
Miyauchi, K.1
Kimura, S.2
Suzuki, T.3
-
27
-
-
0025683270
-
Preparation and enzymatic hydrolysis of DNA and RNA for mass spectrometry
-
Crain, P.F. Preparation and enzymatic hydrolysis of DNA and RNA for mass spectrometry. Methods Enzymol. 193, 782-790 (1990).
-
(1990)
Methods Enzymol.
, vol.193
, pp. 782-790
-
-
Crain, P.F.1
-
28
-
-
84874750617
-
A human tRNA methyltransferase 9-like protein prevents tumour growth by regulating LIN9 and HIF1-α
-
Begley, U. et al. A human tRNA methyltransferase 9-like protein prevents tumour growth by regulating LIN9 and HIF1-α. EMBO Mol. Med. 5, 366-383 (2013).
-
(2013)
EMBO Mol. Med.
, vol.5
, pp. 366-383
-
-
Begley, U.1
-
29
-
-
84865298780
-
Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications
-
Patil, A. et al. Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications. RNA Biol. 9, 990-1001 (2012).
-
(2012)
RNA Biol.
, vol.9
, pp. 990-1001
-
-
Patil, A.1
-
30
-
-
84867259656
-
Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response
-
Patil, A. et al. Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response. Cell Cycle 11, 3656-3665 (2012).
-
(2012)
Cell Cycle
, vol.11
, pp. 3656-3665
-
-
Patil, A.1
-
31
-
-
84866622511
-
The yeast rapid tRNA decay pathway competes with elongation factor 1A for substrate tRNAs and acts on tRNAs lacking one or more of several modifications
-
Dewe, J.M. et al. The yeast rapid tRNA decay pathway competes with elongation factor 1A for substrate tRNAs and acts on tRNAs lacking one or more of several modifications. RNA 18, 1886-1896 (2012).
-
(2012)
RNA
, vol.18
, pp. 1886-1896
-
-
Dewe, J.M.1
-
32
-
-
77956276464
-
TRNA biology charges to the front
-
Phizicky, E.M. & Hopper, A.K. tRNA biology charges to the front. Genes Dev. 24, 1832-1860 (2010).
-
(2010)
Genes Dev.
, vol.24
, pp. 1832-1860
-
-
Phizicky, E.M.1
Hopper, A.K.2
-
33
-
-
80052461558
-
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
-
Ito, S. et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300-1303 (2011).
-
(2011)
Science
, vol.333
, pp. 1300-1303
-
-
Ito, S.1
-
34
-
-
77951981033
-
Human AlkB homolog ABH8 is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival
-
Fu, D. et al. Human AlkB homolog ABH8 is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival. Mol. Cell Biol. 30, 2449-2459 (2010).
-
(2010)
Mol. Cell Biol.
, vol.30
, pp. 2449-2459
-
-
Fu, D.1
-
35
-
-
77949376153
-
Mammalian ALKBH8 possesses tRNA methyltransferase activity required for the biogenesis of multiple wobble uridine modifications implicated in translational decoding
-
Songe-Moller, L. et al. Mammalian ALKBH8 possesses tRNA methyltransferase activity required for the biogenesis of multiple wobble uridine modifications implicated in translational decoding. Mol. Cell Biol. 30, 1814-1827 (2010).
-
(2010)
Mol. Cell Biol.
, vol.30
, pp. 1814-1827
-
-
Songe-Moller, L.1
-
36
-
-
79551582659
-
ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA
-
van den Born, E. et al. ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA. Nat. Commun. 2, 172 (2011).
-
(2011)
Nat. Commun.
, vol.2
, pp. 172
-
-
Van Den Born, E.1
-
37
-
-
0036629250
-
RRNA modifications and ribosome function
-
Decatur, W.A. & Fournier, M.J. rRNA modifications and ribosome function. Trends Biochem. Sci. 27, 344-351 (2002).
-
(2002)
Trends Biochem. Sci.
, vol.27
, pp. 344-351
-
-
Decatur, W.A.1
Fournier, M.J.2
-
38
-
-
84872268888
-
Nucleic acid modifications with epigenetic significance
-
Fu, Y. & He, C. Nucleic acid modifications with epigenetic significance. Curr. Opin. Chem. Biol. 16, 516-524 (2012).
-
(2012)
Curr. Opin. Chem. Biol.
, vol.16
, pp. 516-524
-
-
Fu, Y.1
He, C.2
-
39
-
-
84255209216
-
Cellular dynamics of RNA modification
-
Yi, C. & Pan, T. Cellular dynamics of RNA modification. Acct. Chem. Res. 44, 1380-1388 (2011).
-
(2011)
Acct. Chem. Res.
, vol.44
, pp. 1380-1388
-
-
Yi, C.1
Pan, T.2
-
40
-
-
38649099969
-
Strand-specific 5?-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity
-
Chen, P.Y. et al. Strand-specific 5?-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity. RNA 14, 263-274 (2007).
-
(2007)
RNA
, vol.14
, pp. 263-274
-
-
Chen, P.Y.1
-
41
-
-
26444540413
-
Extensive 3? Modification of plant small RNAs is modulated by helper component-proteinase expression
-
Ebhardt, H.A., Thi, E.P., Wang, M.B. & Unrau, P.J. Extensive 3? modification of plant small RNAs is modulated by helper component-proteinase expression. Proc. Natl. Acad. Sci. USA 102, 13398-13403 (2005).
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 13398-13403
-
-
Ebhardt, H.A.1
Thi, E.P.2
Wang, M.B.3
Unrau, P.J.4
-
42
-
-
61449186404
-
Selective stabilization of mammalian microRNAs by 3? Adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2
-
Katoh, T. et al. Selective stabilization of mammalian microRNAs by 3? adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2. Genes Dev. 23, 433-438 (2009).
-
(2009)
Genes Dev.
, vol.23
, pp. 433-438
-
-
Katoh, T.1
-
43
-
-
0025748046
-
Synthesis and purification of large amounts of RNA oligonucleotides
-
Wyatt, J.R., Chastain, M. & Puglisi, J.D. Synthesis and purification of large amounts of RNA oligonucleotides. Biotechniques 11, 764-769 (1991).
-
(1991)
Biotechniques
, vol.11
, pp. 764-769
-
-
Wyatt, J.R.1
Chastain, M.2
Puglisi, J.D.3
-
44
-
-
1942501609
-
Large-scale preparation and purification of polyacrylamide-free RNA oligonucleotides
-
Lukavsky, P.J. & Puglisi, J.D. Large-scale preparation and purification of polyacrylamide-free RNA oligonucleotides. RNA 10, 889-893 (2004).
-
(2004)
RNA
, vol.10
, pp. 889-893
-
-
Lukavsky, P.J.1
Puglisi, J.D.2
-
45
-
-
0039993541
-
Escherichia coli formylmethionine tRNA: Mutations in GGGCCC sequence conserved in anticodon stem of initiator tRNAs affect initiation of protein synthesis and conformation of anticodon loop
-
Seong, B.L. & RajBhandary, U.L. Escherichia coli formylmethionine tRNA: mutations in GGGCCC sequence conserved in anticodon stem of initiator tRNAs affect initiation of protein synthesis and conformation of anticodon loop. Proc. Natl. Acad. Sci. USA 84, 334-338 (1987).
-
(1987)
Proc. Natl. Acad. Sci. USA
, vol.84
, pp. 334-338
-
-
Seong, B.L.1
Rajbhandary, U.L.2
-
46
-
-
77149143215
-
Rapid, nondenaturing RNA purification using weak anion-exchange fast performance liquid chromatography
-
Easton, L.E., Shibata, Y. & Lukavsky, P.J. Rapid, nondenaturing RNA purification using weak anion-exchange fast performance liquid chromatography. RNA 16, 647-653 (2010).
-
(2010)
RNA
, vol.16
, pp. 647-653
-
-
Easton, L.E.1
Shibata, Y.2
Lukavsky, P.J.3
-
47
-
-
59049088566
-
Studying the mechanism of RNA separations using RNA chromatography and its application in the analysis of ribosomal RNA and RNA:RNA interactions
-
Waghmare, S.P., Pousinis, P., Hornby, D.P. & Dickman, M.J. Studying the mechanism of RNA separations using RNA chromatography and its application in the analysis of ribosomal RNA and RNA:RNA interactions. J. Chromatogr. A 1216, 1377-1382 (2009).
-
(2009)
J. Chromatogr. A
, vol.1216
, pp. 1377-1382
-
-
Waghmare, S.P.1
Pousinis, P.2
Hornby, D.P.3
Dickman, M.J.4
-
48
-
-
41949126478
-
Separation of plant viral satellite double-stranded RNA using high-performance liquid chromatography
-
Likic, S., Rusak, G. & Krajacic, M. Separation of plant viral satellite double-stranded RNA using high-performance liquid chromatography. J. Chromatogr. A 1189, 451-455 (2008).
-
(2008)
J. Chromatogr. A
, vol.1189
, pp. 451-455
-
-
Likic, S.1
Rusak, G.2
Krajacic, M.3
-
49
-
-
33846446409
-
Rapid purification of RNAs using fast performance liquid chromatography (FPLC)
-
Kim, I., McKenna, S.A., Viani Puglisi, E. & Puglisi, J.D. Rapid purification of RNAs using fast performance liquid chromatography (FPLC). RNA 13, 289-294 (2007).
-
(2007)
RNA
, vol.13
, pp. 289-294
-
-
Kim, I.1
McKenna, S.A.2
Viani Puglisi, E.3
Puglisi, J.D.4
-
51
-
-
0021113360
-
Operational variables in high-performance gel filtration of DNA fragments and RNAs
-
Kato, Y. et al. Operational variables in high-performance gel filtration of DNA fragments and RNAs. J. Chromatogr. 266, 341-349 (1983).
-
(1983)
J. Chromatogr.
, vol.266
, pp. 341-349
-
-
Kato, Y.1
-
52
-
-
84884968828
-
A multidimensional platform for the purification of non-coding RNA species
-
Chionh, Y.H. et al. A multidimensional platform for the purification of non-coding RNA species. Nucleic Acids Res. 41, e168 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Chionh, Y.H.1
-
53
-
-
84862991525
-
Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells
-
Kim, Y.K. et al. Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells. Mol. Cell 46, 893-895 (2012).
-
(2012)
Mol. Cell
, vol.46
, pp. 893-895
-
-
Kim, Y.K.1
-
54
-
-
84858330248
-
Importance of RNA isolation methods for analysis of exosomal RNA: Evaluation of different methods
-
Eldh, M., Lotvall, J., Malmhall, C. & Ekstrom, K. Importance of RNA isolation methods for analysis of exosomal RNA: evaluation of different methods. Mol. Immunol. 50, 278-286 (2012).
-
(2012)
Mol. Immunol.
, vol.50
, pp. 278-286
-
-
Eldh, M.1
Lotvall, J.2
Malmhall, C.3
Ekstrom, K.4
-
55
-
-
84867237573
-
Method for microRNA isolation from clinical serum samples
-
Li, Y. & Kowdley, K.V. Method for microRNA isolation from clinical serum samples. Anal. Biochem. 431, 69-75 (2012).
-
(2012)
Anal. Biochem.
, vol.431
, pp. 69-75
-
-
Li, Y.1
Kowdley, K.V.2
-
56
-
-
50349091399
-
Quantification of DNA damage products resulting from deamination, oxidation and reaction with products of lipid peroxidation by liquid chromatography isotope dilution tandem mass spectrometry
-
Taghizadeh, K. et al. Quantification of DNA damage products resulting from deamination, oxidation and reaction with products of lipid peroxidation by liquid chromatography isotope dilution tandem mass spectrometry. Nat. Protoc. 3, 1287-1298 (2008).
-
(2008)
Nat. Protoc.
, vol.3
, pp. 1287-1298
-
-
Taghizadeh, K.1
-
57
-
-
0141848395
-
Absence of 2?-deoxyoxanosine and presence of abasic sites in DNA exposed to nitric oxide at controlled physiological concentrations
-
Dong, M., Wang, C., Deen, W.M. & Dedon, P.C. Absence of 2?-deoxyoxanosine and presence of abasic sites in DNA exposed to nitric oxide at controlled physiological concentrations. Chem. Res. Toxicol. 16, 1044-1055 (2003).
-
(2003)
Chem. Res. Toxicol.
, vol.16
, pp. 1044-1055
-
-
Dong, M.1
Wang, C.2
Deen, W.M.3
Dedon, P.C.4
-
58
-
-
79960896599
-
Identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in E. Coli 23S rRNA
-
Havelund, J.F. et al. Identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in E. coli 23S rRNA. J. Mol. Biol. 411, 529-536 (2011).
-
(2011)
J. Mol. Biol.
, vol.411
, pp. 529-536
-
-
Havelund, J.F.1
|