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1. Full Text Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number
by Pang, Yan Ling Joy and Abo, Ryan and Levine, Stuart S and Dedon, Peter C
Nucleic Acids Research, ISSN 0305-1048, 12/2014, Volume 42, Issue 22, pp. e170 - e170
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2. Full Text Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses
by Chan, Cheryl and Pham, Phuong and Dedon, Peter C and Dedon, Peter C and Begley, Thomas J and Begley, Thomas J
Genome biology, ISSN 1474-7596, 12/2018, Volume 19, Issue 1, pp. 228 - 11
Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level... 
USAGE BIAS | METHYLTRANSFERASE | MESSENGER-RNA | SPECIFICITY | PROTEIN-DEGRADATION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | QUANTIFICATION | ESCHERICHIA-COLI | GENETICS & HEREDITY | GENE-EXPRESSION | OPTIMIZATION | ANTICODON LOOP | Enzymes | Translation | tRNA | Bias | Scheduling | Gene expression | Proteins | E coli | Use statistics | Codon bias | DNA methylation | Hypoxia | Deoxyribonucleic acid--DNA | Viral infections | Transfer RNA
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3. Full Text The m 6 A pathway facilitates sex determination in Drosophila
by Kan, Lijuan and Grozhik, Anya V and Vedanayagam, Jeffrey and Patil, Deepak P and Pang, Nan and Lim, Kok-Seong and Huang, Yi-Chun and Joseph, Brian and Lin, Ching-Jung and Despic, Vladimir and Guo, Jian and Yan, Dong and Kondo, Shu and Deng, Wu-Min and Dedon, Peter C and Jaffrey, Samie R and Lai, Eric C
Nature Communications, 07/2017, Volume 8, p. 15737
The conserved modification N -methyladenosine (m A) modulates mRNA processing and activity. Here, we establish the Drosophila system to study the m A pathway.... 
Multigene Family | Alternative Splicing | Introns | Transcriptome | Male | Drosophila Proteins - metabolism | RNA, Messenger - metabolism | Drosophila melanogaster - genetics | Amino Acid Motifs | Behavior, Animal | DNA Methylation | Phenotype | Animals | Sex Determination Processes | Mutagenesis | Gene Expression Regulation, Developmental | Adenosine - analogs & derivatives | Mass Spectrometry | Female | Adenosine - chemistry | Models, Genetic | Mutation | RNA-Binding Proteins - metabolism | Ovary - metabolism
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4. Full Text Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA
by Wang, Jin and Alvin Chew, Bing Liang and Lai, Yong and Dong, Hongping and Xu, Luang and Balamkundu, Seetharamsingh and Cai, Weiling Maggie and Cui, Liang and Liu, Chuan Fa and Fu, Xin-Yuan and Lin, Zhenguo and Shi, Pei-Yong and Lu, Timothy K and Luo, Dahai and Jaffrey, Samie R and Dedon, Peter C
Nucleic acids research, ISSN 0305-1048, 09/2019
Chemical modification of transcripts with 5' caps occurs in all organisms. Here, we report a systems-level mass spectrometry-based technique, CapQuant, for... 
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5. Full Text The chemical toxicology of 2-deoxyribose oxidation in DNA
by Dedon, Peter C
Chemical Research in Toxicology, ISSN 0893-228X, 01/2008, Volume 21, Issue 1, pp. 206 - 219
Damage to DNA and RNA caused by oxidative mechanisms has been well-studied for its potential role in the development of human disease. Only recently, though,... 
CHEMISTRY, MEDICINAL | HYDROGEN-ATOM ABSTRACTION | ESCHERICHIA-COLI | RAT-LIVER NUCLEI | PROTEIN CROSS-LINKS | CHEMISTRY, MULTIDISCIPLINARY | DOUBLE-STRAND CLEAVAGE | 1,10-PHENANTHROLINE COPPER-ION | GAS-CHROMATOGRAPHY | CAPTURE MASS-SPECTROMETRY | TOXICOLOGY | GLUTATHIONE-S-TRANSFERASE | EXCISION-REPAIR ENZYMES | Solvents | DNA - chemistry | Animals | Models, Chemical | Oxidation-Reduction | Glutathione - metabolism | Humans | Deoxyribose - chemistry | Glutathione Transferase - metabolism | DNA Damage | RNA - drug effects | DNA - drug effects
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6. Full Text Reactive species and DNA damage in chronic inflammation: reconciling chemical mechanisms and biological fates
by Lonkar, Pallavi and Dedon, Peter C
International Journal of Cancer, ISSN 0020-7136, 05/2011, Volume 128, Issue 9, pp. 1999 - 2009
Chronic inflammation has long been recognized as a risk factor for many human cancers. One mechanistic link between inflammation and cancer involves the... 
nitric oxide | inflammation | DNA damage | macrophage | metabolism | superoxide | biomarker | lipid peroxidation | neutrophil | Biomarker | Nitric oxide | Lipid peroxidation | Inflammation | Superoxide | Neutrophil | Metabolism | Macrophage | CROSS-LINK FORMATION | BASE-EXCISION-REPAIR | TANDEM MASS-SPECTROMETRY | ONCOLOGY | MALONDIALDEHYDE-DEOXYGUANOSINE ADDUCT | POLYUNSATURATED FATTY-ACIDS | TYPHIMURIUM HISD3052 GENE | (CPG) FRAMESHIFT HOTSPOT | FLUKE-INFECTED PATIENTS | RNA-EDITING ENZYMES | CALF THYMUS DNA | Inflammation - metabolism | Animals | Reactive Oxygen Species - metabolism | Neoplasms - genetics | Reactive Nitrogen Species - adverse effects | Cell Transformation, Neoplastic - genetics | Humans | Risk Factors | DNA Damage - genetics | Inflammation - genetics | Chronic Disease | Urine | Oxidative stress | Excretion | Oxygen | biomarkers | Leukocytes (neutrophilic) | nucleic acids | Macrophages | Nitrogen | Carcinogenesis | Blood | Risk factors | Signal transduction | biotransformation | Apoptosis | Cancer | Index Medicus
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7. Full Text Three distinct 3-methylcytidine (m3C) methyltransferases modify tRNA and mRNA in mice and humans
by Xu, Luang and Liu, Xinyu and Sheng, Na and Oo, Kyaw Soe and Liang, Junxin and Chionh, Yok Hian and Xu, Juan and Ye, Fuzhou and Gao, Yong-Gui and Dedon, Peter C and Fu, Xin-Yuan
Journal of Biological Chemistry, ISSN 0021-9258, 2017, Volume 292, Issue 35, pp. 14695 - 14703
Chemical RNA modifications are central features of epitranscriptomics, highlighted by the discovery of modified ribonucleosides in mRNA and exemplified by the... 
Liver - enzymology | Humans | Methyltransferases - metabolism | Methyltransferases - genetics | Substrate Specificity | Serine-tRNA Ligase - chemistry | Cytidine - analogs & derivatives | RNA, Messenger - metabolism | Recombinant Fusion Proteins - metabolism | Serine-tRNA Ligase - metabolism | RNA Interference | Isoenzymes - metabolism | Mice, Mutant Strains | RNA, Transfer, Arg - metabolism | Cell Line | Methyltransferases - chemistry | RNA Processing, Post-Transcriptional | RNA, Transfer, Thr - metabolism | Isoenzymes - genetics | RNA, Transfer - metabolism | Liver - metabolism | Recombinant Fusion Proteins - chemistry | Mice, Knockout | Animals | Methyltransferases - antagonists & inhibitors | Cytidine - metabolism | Mice | RNA, Transfer, Ser - metabolism | Mutation | Methylation | Editors' Picks | mouse | Mettl2 | transfer RNA (tRNA) | Mettl6 | RNA methyltransferase | mRNA | m3C | human | mice | Mettl8
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8. Full Text tRNA modifications regulate translation during cellular stress
by Gu, Chen and Begley, Thomas J and Dedon, Peter C
FEBS Letters, ISSN 0014-5793, 11/2014, Volume 588, Issue 23, pp. 4287 - 4296
The regulation of gene expression in response to stress is an essential cellular protection mechanism. Recent advances in tRNA modification analysis and... 
Translation | Modified ribonucleoside | Stress response | Codon usage | Transfer RNA | OXIDATIVE STRESS | DNA-DAMAGE RESPONSE | BIOCHEMISTRY & MOLECULAR BIOLOGY | TUMOR-SUPPRESSOR GENE | SACCHAROMYCES-CEREVISIAE | MODIFYING ENZYMES | CELL BIOLOGY | UNFOLDED PROTEIN RESPONSE | BIOPHYSICS | SHORT ARM | CHRONIC INFLAMMATION | METHYLTRANSFERASE TRMD | Protein Biosynthesis | Animals | Disease - genetics | Stress, Physiological - genetics | Humans | Cells - metabolism | RNA, Transfer - genetics | Genetic translation | Analysis | Genomics | translation | stress response | transfer RNA | modified ribonucleoside | codon usage
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9. Metabolic fate of endogenous molecular damage: Urinary glutathione conjugates of DNA-derived base propenals as markers of inflammation
by Jumpathong, Watthanachai and Chan, Wan and Taghizadeh, Koli and Babu, I Ramesh and Dedon, Peter C
Proceedings of the National Academy of Sciences, USA, ISSN 0027-8424, 09/2015, Volume 112, Issue 35, pp. E4845 - E4845
Although mechanistically linked to disease, cellular molecules damaged by endogenous processes have not emerged as significant biomarkers of inflammation and... 
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10. Full Text Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response inPseudomonas aeruginosa
by Jaroensuk, Juthamas and Atichartpongkul, Sopapan and Chionh, Yok Hian and Wong, Yee Hwa and Liew, Chong Wai and McBee, Megan E and Thongdee, Narumon and Prestwich, Erin G and DeMott, Michael S and Mongkolsuk, Skorn and Dedon, Peter C and Lescar, Julien and Fuangthong, Mayuree
Nucleic Acids Research, ISSN 0305-1048, 12/2016, Volume 44, Issue 22, pp. 10834 - 10848
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11. Full Text The Versatile Roles of the tRNA Epitranscriptome during Cellular Responses to Toxic Exposures and Environmental Stress
by Huber, Sabrina M and Leonardi, Andrea and Dedon, Peter C and Begley, Thomas J
Toxics, ISSN 2305-6304, 03/2019, Volume 7, Issue 1, p. 17
Living organisms respond to environmental changes and xenobiotic exposures by regulating gene expression. While heat shock, unfolded protein, and DNA damage... 
stress response mechanisms | tRNA modifications | epitranscriptomics | codon-biased translation
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12. Novel genomic island modifies DNA with 7-deazaguanine derivatives
by Thiaville, Jennifer J and Kellner, Stefanie M and Yuan, Yifeng and Hutinet, Geoffrey and Thiaville, Patrick C and Jumpathong, Watthanachai and Mohapatra, Susovan and Brochier-Armanet, Celine and Letarov, Andrey V and Hillebrand, Roman and Malik, Chanchal K and Rizzo, Carmelo J and Dedon, Peter C and de Crecy-Lagard, Valerie
Proceedings of the National Academy of Sciences, USA, ISSN 0027-8424, 03/2016, Volume 113, Issue 11, pp. E1452 - E1452
The discovery of ~20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine... 
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13. Full Text A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress
by Chan, Clement T. Y and Dyavaiah, Madhu and DeMott, Michael S and Taghizadeh, Koli and Dedon, Peter C and Begley, Thomas J
PLoS Genetics, ISSN 1553-7390, 12/2010, Volume 6, Issue 12, pp. 1 - 9
Decades of study have revealed more than 100 ribonucleoside structures incorporated as post-transcriptional modifications mainly in tRNA and rRNA, yet the... 
YEAST | DNA-DAMAGING AGENTS | WOBBLE POSITION | HYPOCHLOROUS ACID | GENETICS & HEREDITY | MODIFIED NUCLEOSIDES | CYTOPLASMIC TRANSFER-RNA | IDENTIFICATION | SACCHAROMYCES-CEREVISIAE | MASS-SPECTROMETRY | GENOME | Saccharomyces cerevisiae - cytology | Saccharomyces cerevisiae - metabolism | RNA, Transfer - genetics | RNA Processing, Post-Transcriptional | RNA, Transfer - metabolism | Stress, Physiological | Physiological aspects | Genetic aspects | Research | Brewer's yeast | Cells | Transfer RNA | Health sciences | Yeast | Environmental health | Genetics | Cytotoxicity | Principal components analysis | Stress response
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