Published in J Mol Biol on November 15, 2006
The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res (2010) 3.42
A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genet (2010) 2.73
tRNA's modifications bring order to gene expression. Curr Opin Microbiol (2008) 2.51
MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor. Plant Cell (2008) 2.38
Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1. Genes Dev (2008) 2.28
How mutations in tRNA distant from the anticodon affect the fidelity of decoding. Nat Struct Mol Biol (2011) 2.10
Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. EMBO Rep (2008) 1.98
Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat Commun (2012) 1.93
A conserved modified wobble nucleoside (mcm5s2U) in lysyl-tRNA is required for viability in yeast. RNA (2007) 1.88
Human tRNA(Lys3)(UUU) is pre-structured by natural modifications for cognate and wobble codon binding through keto-enol tautomerism. J Mol Biol (2011) 1.82
Discovery and biological characterization of geranylated RNA in bacteria. Nat Chem Biol (2012) 1.70
Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine. Nucleic Acids Res (2007) 1.66
Yeast targets for mRNA methylation. Nucleic Acids Res (2010) 1.63
Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Nat Struct Mol Biol (2007) 1.58
Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival. Mol Cell Biol (2010) 1.53
The conserved Wobble uridine tRNA thiolase Ctu1-Ctu2 is required to maintain genome integrity. Proc Natl Acad Sci U S A (2008) 1.50
Do all modifications benefit all tRNAs? FEBS Lett (2010) 1.46
Translational selection is ubiquitous in prokaryotes. PLoS Genet (2010) 1.45
Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res (2013) 1.44
Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages. Nucleic Acids Res (2010) 1.42
The crystal structure and small-angle X-ray analysis of CsdL/TcdA reveal a new tRNA binding motif in the MoeB/E1 superfamily. PLoS One (2015) 1.41
Retracted Loss of a Conserved tRNA Anticodon Modification Perturbs Plant Immunity. PLoS Genet (2015) 1.41
Translational control of cell division by Elongator. Cell Rep (2012) 1.41
Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity. Cell (2015) 1.39
Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J Biol Chem (2012) 1.38
Loss of a conserved tRNA anticodon modification perturbs cellular signaling. PLoS Genet (2013) 1.37
Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases. J Mol Biol (2007) 1.37
Transfer RNA modifications: nature's combinatorial chemistry playground. Wiley Interdiscip Rev RNA (2012) 1.37
Haloquadratum walsbyi: limited diversity in a global pond. PLoS One (2011) 1.37
Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import. Proc Natl Acad Sci U S A (2008) 1.32
RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation. Genes Dev (2015) 1.29
Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy. Nucleic Acids Res (2009) 1.27
A compendium of human mitochondrial gene expression machinery with links to disease. Environ Mol Mutagen (2010) 1.26
Genetic analysis of the E site during RF2 programmed frameshifting. RNA (2007) 1.23
tRNA tKUUU, tQUUG, and tEUUC wobble position modifications fine-tune protein translation by promoting ribosome A-site binding. Proc Natl Acad Sci U S A (2013) 1.23
Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids. BMC Genomics (2008) 1.22
Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias. PLoS Genet (2010) 1.21
Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains. Science (2015) 1.21
The Sua5 protein is essential for normal translational regulation in yeast. Mol Cell Biol (2010) 1.21
Differentiating between near- and non-cognate codons in Saccharomyces cerevisiae. PLoS One (2007) 1.17
Role of the ubiquitin-like protein Urm1 as a noncanonical lysine-directed protein modifier. Proc Natl Acad Sci U S A (2011) 1.16
The many applications of acid urea polyacrylamide gel electrophoresis to studies of tRNAs and aminoacyl-tRNA synthetases. Methods (2008) 1.15
Free energy calculation of modified base-pair formation in explicit solvent: A predictive model. RNA (2009) 1.15
Modification of tRNA(Lys) UUU by elongator is essential for efficient translation of stress mRNAs. PLoS Genet (2013) 1.14
Mitochondrial tRNA import--the challenge to understand has just begun. Biol Chem (2009) 1.13
Codon Bias as a Means to Fine-Tune Gene Expression. Mol Cell (2015) 1.11
Comprehensive survey and geometric classification of base triples in RNA structures. Nucleic Acids Res (2011) 1.11
Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana. BMC Genomics (2009) 1.11
Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase. Nucleic Acids Res (2010) 1.10
Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. Nat Protoc (2014) 1.09
Optimization of the hybridization-based method for purification of thermostable tRNAs in the presence of tetraalkylammonium salts. Nucleic Acids Res (2009) 1.09
Defects in purine nucleotide metabolism lead to substantial incorporation of xanthine and hypoxanthine into DNA and RNA. Proc Natl Acad Sci U S A (2012) 1.07
Darwinian behavior in a cold, sporadically fed pool of ribonucleotides. Astrobiology (2012) 1.06
Arabidopsis tRNA adenosine deaminase arginine edits the wobble nucleotide of chloroplast tRNAArg(ACG) and is essential for efficient chloroplast translation. Plant Cell (2009) 1.06
Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop. RNA (2012) 1.05
Combination of the loss of cmnm5U34 with the lack of s2U34 modifications of tRNALys, tRNAGlu, and tRNAGln altered mitochondrial biogenesis and respiration. J Mol Biol (2009) 1.04
tRNAomics: tRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote. RNA (2012) 1.04
The human mitochondrial tRNAMet: structure/function relationship of a unique modification in the decoding of unconventional codons. J Mol Biol (2010) 1.03
The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy. RNA (2012) 1.03
Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy. PLoS Biol (2009) 1.01
Cluster M mycobacteriophages Bongo, PegLeg, and Rey with unusually large repertoires of tRNA isotypes. J Virol (2013) 1.01
Bases in the anticodon loop of tRNA(Ala)(GGC) prevent misreading. Nat Struct Mol Biol (2009) 1.00
RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon. EMBO J (2009) 0.99
Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number. Nucleic Acids Res (2014) 0.98
Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis. Genes Dev (2014) 0.98
Archaeal ubiquitin-like proteins: functional versatility and putative ancestral involvement in tRNA modification revealed by comparative genomic analysis. Archaea (2010) 0.97
Thiolation controls cytoplasmic tRNA stability and acts as a negative determinant for tRNA editing in mitochondria. J Biol Chem (2009) 0.97
NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation. EMBO J (2016) 0.96
Lack of tRNA modification isopentenyl-A37 alters mRNA decoding and causes metabolic deficiencies in fission yeast. Mol Cell Biol (2013) 0.95
Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome. RNA (2011) 0.94
RNA-protein mutually induced fit: structure of Escherichia coli isopentenyl-tRNA transferase in complex with tRNA(Phe). J Biol Chem (2009) 0.94
The yfiC gene of E. coli encodes an adenine-N6 methyltransferase that specifically modifies A37 of tRNA1Val(cmo5UAC). RNA (2009) 0.94
Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon. RNA (2008) 0.94
Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases. RNA (2011) 0.94
tRNA structural and functional changes induced by oxidative stress. Cell Mol Life Sci (2011) 0.93
Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses. RNA Biol (2015) 0.92
Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon. Biochemistry (2009) 0.92
A coordinated codon-dependent regulation of translation by Elongator. Cell Cycle (2012) 0.92
Systematic identification of tRNAome and its dynamics in Lactococcus lactis. Mol Microbiol (2014) 0.92
Nonsense and sense suppression abilities of original and derivative Methanosarcina mazei pyrrolysyl-tRNA synthetase-tRNA(Pyl) pairs in the Escherichia coli BL21(DE3) cell strain. PLoS One (2013) 0.92
Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes. Chem Res Toxicol (2015) 0.92
Rectifier of aberrant mRNA splicing recovers tRNA modification in familial dysautonomia. Proc Natl Acad Sci U S A (2015) 0.91
Transfer RNA misidentification scrambles sense codon recoding. Chembiochem (2013) 0.91
Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae. RNA (2011) 0.91
Defects in tRNA Anticodon Loop 2'-O-Methylation Are Implicated in Nonsyndromic X-Linked Intellectual Disability due to Mutations in FTSJ1. Hum Mutat (2015) 0.91
An integrated, structure- and energy-based view of the genetic code. Nucleic Acids Res (2016) 0.89
Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage. Nucleic Acids Res (2009) 0.89
Structure and function of preQ1 riboswitches. Biochim Biophys Acta (2014) 0.89
Evaluating the reproducibility of quantifying modified nucleosides from ribonucleic acids by LC-UV-MS. J Chromatogr B Analyt Technol Biomed Life Sci (2013) 0.88
tRNA thiolation links translation to stress responses in Saccharomyces cerevisiae. Mol Biol Cell (2014) 0.88
Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t(6)A), a universal modification of tRNA. RNA Biol (2014) 0.88
Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons. RNA (2012) 0.88
A critical analysis of codon optimization in human therapeutics. Trends Mol Med (2014) 0.88
Functional Analysis of Bacillus subtilis Genes Involved in the Biosynthesis of 4-Thiouridine in tRNA. J Bacteriol (2012) 0.87
Endonuclease V cleaves at inosines in RNA. Nat Commun (2013) 0.87
Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism. Genome Biol (2015) 0.87
In vivo identification of essential nucleotides in tRNALeu to its functions by using a constructed yeast tRNALeu knockout strain. Nucleic Acids Res (2012) 0.87
The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res (2010) 3.42
Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Nat Struct Mol Biol (2007) 1.58
Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA. Nucleic Acids Res (2010) 1.05
Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNAMet. Nucleic Acids Res (2008) 1.02
Anticodon domain modifications contribute order to tRNA for ribosome-mediated codon binding. Biochemistry (2008) 1.01
The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs. Nucleic Acids Res (2009) 0.94
Different modes of binding of mono-, di-, and trihalogenated phenols to the hemoglobin dehaloperoxidase from Amphitrite ornata. Biochemistry (2009) 0.88
A disease-causing point mutation in human mitochondrial tRNAMet rsults in tRNA misfolding leading to defects in translational initiation and elongation. J Biol Chem (2008) 0.87
NMR studies of the inclusion complex of cloprostenol sodium salt with beta-cyclodextrin in aqueous solution. Pharm Res (2007) 0.75