Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses

[1]  Sebastian A. Leidel,et al.  Codon-specific translation reprogramming promotes resistance to targeted therapy , 2018, Nature.

[2]  L. P. Sarin,et al.  Transfer RNA modification and infection - Implications for pathogenicity and host responses. , 2018, Biochimica et biophysica acta. Gene regulatory mechanisms.

[3]  K. Becker,et al.  Elongator and codon bias regulate protein levels in mammalian peripheral neurons , 2018, Nature Communications.

[4]  Cara T. Pager,et al.  Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection , 2018, Nucleic acids research.

[5]  Samie R. Jaffrey,et al.  Reading m6A in the Transcriptome: m6A-Binding Proteins. , 2017, Trends in cell biology.

[6]  Tony Gutschner,et al.  The Dark Side of the Epitranscriptome: Chemical Modifications in Long Non-Coding RNAs , 2017, International journal of molecular sciences.

[7]  Hailing Shi,et al.  Epitranscriptomic influences on development and disease , 2017, Genome Biology.

[8]  Chuan He,et al.  The emerging biology of RNA post-transcriptional modifications , 2017, RNA biology.

[9]  R. Klassen,et al.  Independent suppression of ribosomal +1 frameshifts by different tRNA anticodon loop modifications , 2016, RNA biology.

[10]  Thomas J. Begley,et al.  tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence , 2016, Nature Communications.

[11]  Sebastian A. Leidel,et al.  Elp3 links tRNA modification to IRES-dependent translation of LEF1 to sustain metastasis in breast cancer , 2016, The Journal of experimental medicine.

[12]  F. Tuorto,et al.  Genome recoding by tRNA modifications , 2016, Open Biology.

[13]  M. Helm,et al.  Analysis of RNA modifications by liquid chromatography-tandem mass spectrometry. , 2016, Methods.

[14]  P. Limbach,et al.  Sequence mapping of transfer RNA chemical modifications by liquid chromatography tandem mass spectrometry. , 2016, Methods.

[15]  G. Randall,et al.  Flavivirus modulation of cellular metabolism. , 2016, Current opinion in virology.

[16]  E. Westhof,et al.  An integrated, structure- and energy-based view of the genetic code , 2016, Nucleic acids research.

[17]  Scott B. Dewell,et al.  Greater Than the Sum of Parts: Complexity of the Dynamic Epigenome. , 2016, Molecular cell.

[18]  Henrik Molina,et al.  Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression , 2016, Cell.

[19]  L. S. Churchman,et al.  Synchronized translation programs across compartments during mitochondrial biogenesis , 2016 .

[20]  Thomas J. Begley,et al.  Gene- and genome-based analysis of significant codon patterns in yeast, rat and mice genomes with the CUT Codon UTilization tool. , 2016, Methods.

[21]  B. Nawrot,et al.  Nucleoside modifications in the regulation of gene expression: focus on tRNA , 2016, Cellular and Molecular Life Sciences.

[22]  Andrea du Toit.  Expanding the mRNA epitranscriptome , 2016, Nature Reviews Molecular Cell Biology.

[23]  Robert D. Finn,et al.  The Dfam database of repetitive DNA families , 2015, Nucleic Acids Res..

[24]  S. Temple,et al.  Attomole quantification and global profile of RNA modifications: Epitranscriptome of human neural stem cells , 2015, Nucleic acids research.

[25]  Walter N. Moss,et al.  Probing Xist RNA Structure in Cells Using Targeted Structure-Seq , 2015, PLoS genetics.

[26]  Thomas J. Begley,et al.  Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation , 2015, PLoS genetics.

[27]  D. Söll,et al.  Codon Bias as a Means to Fine-Tune Gene Expression. , 2015, Molecular cell.

[28]  Thomas J. Begley,et al.  Alkbh8 Regulates Selenocysteine-Protein Expression to Protect against Reactive Oxygen Species Damage , 2015, PloS one.

[29]  Julie L. Chaney,et al.  Roles for Synonymous Codon Usage in Protein Biogenesis. , 2015, Annual review of biophysics.

[30]  Sebastian A. Leidel,et al.  Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity , 2015, Cell.

[31]  Patrick G. A. Pedrioli,et al.  Protein degradation and dynamic tRNA thiolation fine-tune translation at elevated temperatures , 2015, Nucleic acids research.

[32]  D. Drummond,et al.  Correction: A Nutrient-Driven tRNA Modification Alters Translational Fidelity and Genome-wide Protein Coding across an Animal Genus , 2015, PLoS biology.

[33]  P. Farabaugh,et al.  Erratum for Lamichhane et al., Lack of tRNA Modification Isopentenyl-A37 Alters mRNA Decoding and Causes Metabolic Deficiencies in Fission Yeast , 2015, Molecular and Cellular Biology.

[34]  Clement T Y Chan,et al.  Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes , 2015, Chemical research in toxicology.

[35]  H. Ploegh,et al.  tRNA thiolation links translation to stress responses in Saccharomyces cerevisiae , 2015, Molecular biology of the cell.

[36]  M. Curcio,et al.  Global Epitranscriptomics Profiling of RNA Post-Transcriptional Modifications as an Effective Tool for Investigating the Epitranscriptomics of Stress Response* , 2015, Molecular & Cellular Proteomics.

[37]  Thomas J. Begley,et al.  A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications. , 2015, Methods in enzymology.

[38]  D. Drummond,et al.  A Nutrient-Driven tRNA Modification Alters Translational Fidelity and Genome-wide Protein Coding across an Animal Genus , 2014, PLoS biology.

[39]  Dong-Yup Lee,et al.  Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design , 2014, Bioinform..

[40]  R. Maraia,et al.  Different types of secondary information in the genetic code , 2014, RNA.

[41]  Samie R. Jaffrey,et al.  The dynamic epitranscriptome: N6-methyladenosine and gene expression control , 2014, Nature Reviews Molecular Cell Biology.

[42]  Clement T Y Chan,et al.  Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry , 2014, Nature Protocols.

[43]  B. Tu,et al.  Sulfur Amino Acids Regulate Translational Capacity and Metabolic Homeostasis through Modulation of tRNA Thiolation , 2013, Cell.

[44]  Patrick G. A. Pedrioli,et al.  tRNA tKUUU, tQUUG, and tEUUC wobble position modifications fine-tune protein translation by promoting ribosome A-site binding , 2013, Proceedings of the National Academy of Sciences.

[45]  Sebastian A. Leidel,et al.  Modification of tRNALys UUU by Elongator Is Essential for Efficient Translation of Stress mRNAs , 2013, PLoS genetics.

[46]  A. Ciechanover.  Intracellular protein degradation: from a vague idea through the lysosome and the ubiquitin-proteasome system and onto human diseases and drug targeting. , 2013, Bioorganic & medicinal chemistry.

[47]  M. Selbach,et al.  Corrigendum: Global quantification of mammalian gene expression control , 2013, Nature.

[48]  J. Bujnicki,et al.  MODOMICS: a database of RNA modification pathways—2013 update , 2012, Nucleic Acids Res..

[49]  D. Hermand,et al.  A coordinated codon-dependent regulation of translation by Elongator , 2012, Cell cycle.

[50]  A. Benítez-Páez,et al.  The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy. , 2012, RNA.

[51]  Ashish Patil,et al.  Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response , 2012, Cell cycle.

[52]  T. Gedeon,et al.  Delayed protein synthesis reduces the correlation between mRNA and protein fluctuations. , 2012, Biophysical journal.

[53]  Ashish Patil,et al.  Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications , 2012, RNA biology.

[54]  Damien Hermand,et al.  Translational control of cell division by Elongator. , 2012, Cell reports.

[55]  David C. Chang,et al.  2′-O Methylation of Internal Adenosine by Flavivirus NS5 Methyltransferase , 2012, PLoS pathogens.

[56]  T. Pan,et al.  A Role for tRNA Modifications in Genome Structure and Codon Usage , 2012, Cell.

[57]  T. Dick,et al.  How Mycobacterium tuberculosis goes to sleep: the dormancy survival regulator DosR a decade later. , 2012, Future microbiology.

[58]  Jianzhi Zhang,et al.  Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency , 2012, PLoS genetics.

[59]  Clement T Y Chan,et al.  Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins , 2012, Nature Communications.

[60]  M. Selbach,et al.  Global quantification of mammalian gene expression control , 2011, Nature.

[61]  Y. Pilpel,et al.  Determinants of translation efficiency and accuracy , 2011, Molecular systems biology.

[62]  Jef Rozenski,et al.  The RNA modification database, RNAMDB: 2011 update , 2010, Nucleic Acids Res..

[63]  Clement T Y Chan,et al.  A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress , 2010, PLoS genetics.

[64]  J. Powell,et al.  On the Possible Role of tRNA Base Modifications in the Evolution of Codon Usage: Queuosine and Drosophila , 2010, Journal of Molecular Evolution.

[65]  Michal Linial,et al.  Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences , 2009, Molecular systems biology.

[66]  A. Bird,et al.  DNA methylation landscapes: provocative insights from epigenomics , 2008, Nature Reviews Genetics.

[67]  W. Filipowicz,et al.  Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? , 2008, Nature Reviews Genetics.

[68]  Thomas J. Begley,et al.  Trm9-catalyzed tRNA modifications link translation to the DNA damage response. , 2007, Molecular cell.

[69]  Tsutomu Suzuki,et al.  Mass spectrometric identification and characterization of RNA-modifying enzymes. , 2007, Methods in enzymology.

[70]  Weifeng Gu,et al.  Rapid tRNA decay can result from lack of nonessential modifications. , 2006, Molecular cell.

[71]  JamesC . Anderson,et al.  The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans. , 2005, RNA.

[72]  D. Davis,et al.  Structural effects of hypermodified nucleosides in the Escherichia coli and human tRNALys anticodon loop: the effect of nucleosides s2U, mcm5U, mcm5s2U, mnm5s2U, t6A, and ms2t6A. , 2005, Biochemistry.

[73]  P. Sharp,et al.  Variation in the strength of selected codon usage bias among bacteria , 2005, Nucleic acids research.

[74]  J. Elf,et al.  Selective charging of tRNA isoacceptors induced by amino‐acid starvation , 2005, EMBO reports.

[75]  E. O’Shea,et al.  Global analysis of protein expression in yeast , 2003, Nature.

[76]  R. Kliman,et al.  Selection Conflicts, Gene Expression, and Codon Usage Trends in Yeast , 2003, Journal of Molecular Evolution.

[77]  R. Guigó,et al.  Characterization of Mammalian Selenoproteomes , 2003, Science.

[78]  Vadim N. Gladyshev,et al.  Mammalian Selenoprotein in Which Selenocysteine (Sec) Incorporation Is Supported by a New Form of Sec Insertion Sequence Element , 2002, Molecular and Cellular Biology.

[79]  Toshimichi Ikemura,et al.  Codon usage tabulated from international DNA sequence databases: status for the year 2000 , 2000, Nucleic Acids Res..

[80]  V. Gladyshev,et al.  Selenocysteine-containing proteins in mammals. , 1999, Journal of biomedical science.

[81]  A. Hinnebusch,et al.  The essential Gcd10p-Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA. , 1998, Genes & development.

[82]  J. Ofengand,et al.  A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi 746 in 23S RNA is also specific for psi 32 in tRNA(phe). , 1995, RNA.

[83]  P. Sharp,et al.  The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. , 1987, Nucleic acids research.