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Items: 1 to 50 of 153

1.

Backbone resonance assignment for the N-terminal region of bacterial tRNA-(N1G37) methyltransferase.

Li Y, Zhong W, Koay AZ, Ng HQ, Koh-Stenta X, Nah Q, Lim SH, Larsson A, Lescar J, Hill J, Dedon PC, Kang C.

Biomol NMR Assign. 2018 Oct 8. doi: 10.1007/s12104-018-9849-9. [Epub ahead of print]

PMID:
30298375
2.

DNA phosphorothioate modification - a new multi-functional epigenetic system in bacteria.

Wang L, Jiang S, Deng Z, Dedon PC, Chen S.

FEMS Microbiol Rev. 2018 Oct 4. doi: 10.1093/femsre/fuy036. [Epub ahead of print]

PMID:
30289455
3.

tRNA epitranscriptomics and biased codon are linked to proteome expression in Plasmodium falciparum.

Ng CS, Sinha A, Aniweh Y, Nah Q, Babu IR, Gu C, Chionh YH, Dedon PC, Preiser PR.

Mol Syst Biol. 2018 Oct 4;14(10):e8009. doi: 10.15252/msb.20178009.

4.

Aristolochic Acids as Persistent Soil Pollutants: Determination of Risk for Human Exposure and Nephropathy from Plant Uptake.

Li W, Chan CK, Liu Y, Yao J, Mitić B, Kostić EN, Milosavljević B, Davinić I, Orem WH, Tatu CA, Dedon PC, Pavlović NM, Chan W.

J Agric Food Chem. 2018 Oct 18. doi: 10.1021/acs.jafc.8b04770. [Epub ahead of print]

PMID:
30286603
5.

Identification of the minimal bacterial 2'-deoxy-7-amido-7-deazaguanine synthesis machinery.

Yuan Y, Hutinet G, Valera JG, Hu J, Hillebrand R, Gustafson A, Iwata-Reuyl D, Dedon PC, de Crécy-Lagard V.

Mol Microbiol. 2018 Aug 29. doi: 10.1111/mmi.14113. [Epub ahead of print]

PMID:
30159947
6.

Phosphorylation of human TRM9L integrates multiple stress-signaling pathways for tumor growth suppression.

Gu C, Ramos J, Begley U, Dedon PC, Fu D, Begley TJ.

Sci Adv. 2018 Jul 11;4(7):eaas9184. doi: 10.1126/sciadv.aas9184. eCollection 2018 Jul.

7.

Mycobacterium tuberculosis Transfer RNA Induces IL-12p70 via Synergistic Activation of Pattern Recognition Receptors within a Cell Network.

Keegan C, Krutzik S, Schenk M, Scumpia PO, Lu J, Pang YLJ, Russell BS, Lim KS, Shell S, Prestwich E, Su D, Elashoff D, Hershberg RM, Bloom BR, Belisle JT, Fortune S, Dedon PC, Pellegrini M, Modlin RL.

J Immunol. 2018 May 1;200(9):3244-3258. doi: 10.4049/jimmunol.1701733. Epub 2018 Apr 2.

PMID:
29610140
8.

Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis.

Zhong W, Cui L, Goh BC, Cai Q, Ho P, Chionh YH, Yuan M, Sahili AE, Fothergill-Gilmore LA, Walkinshaw MD, Lescar J, Dedon PC.

Nat Commun. 2017 Dec 7;8(1):1986. doi: 10.1038/s41467-017-02086-y.

9.

Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly.

Braun DA, Rao J, Mollet G, Schapiro D, Daugeron MC, Tan W, Gribouval O, Boyer O, Revy P, Jobst-Schwan T, Schmidt JM, Lawson JA, Schanze D, Ashraf S, Ullmann JFP, Hoogstraten CA, Boddaert N, Collinet B, Martin G, Liger D, Lovric S, Furlano M, Guerrera IC, Sanchez-Ferras O, Hu JF, Boschat AC, Sanquer S, Menten B, Vergult S, De Rocker N, Airik M, Hermle T, Shril S, Widmeier E, Gee HY, Choi WI, Sadowski CE, Pabst WL, Warejko JK, Daga A, Basta T, Matejas V, Scharmann K, Kienast SD, Behnam B, Beeson B, Begtrup A, Bruce M, Ch'ng GS, Lin SP, Chang JH, Chen CH, Cho MT, Gaffney PM, Gipson PE, Hsu CH, Kari JA, Ke YY, Kiraly-Borri C, Lai WM, Lemyre E, Littlejohn RO, Masri A, Moghtaderi M, Nakamura K, Ozaltin F, Praet M, Prasad C, Prytula A, Roeder ER, Rump P, Schnur RE, Shiihara T, Sinha MD, Soliman NA, Soulami K, Sweetser DA, Tsai WH, Tsai JD, Topaloglu R, Vester U, Viskochil DH, Vatanavicharn N, Waxler JL, Wierenga KJ, Wolf MTF, Wong SN, Leidel SA, Truglio G, Dedon PC, Poduri A, Mane S, Lifton RP, Bouchard M, Kannu P, Chitayat D, Magen D, Callewaert B, van Tilbeurgh H, Zenker M, Antignac C, Hildebrandt F.

Nat Genet. 2017 Oct;49(10):1529-1538. doi: 10.1038/ng.3933. Epub 2017 Aug 14.

10.

The t6A modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in Streptococcus mutans.

Bacusmo JM, Orsini SS, Hu J, DeMott M, Thiaville PC, Elfarash A, Paulines MJ, Rojas-Benítez D, Meineke B, Deutsch C, Iwata-Reuyl D, Limbach PA, Dedon PC, Rice KC, Shuman S, Crécy-Lagard V.

RNA Biol. 2018;15(4-5):508-517. doi: 10.1080/15476286.2017.1353861. Epub 2017 Sep 13.

11.

N6-Formyllysine as a Biomarker of Formaldehyde Exposure: Formation and Loss of N6-Formyllysine in Nasal Epithelium in Long-Term, Low-Dose Inhalation Studies in Rats.

Edrissi B, Taghizadeh K, Moeller BC, Yu R, Kracko D, Doyle-Eisele M, Swenberg JA, Dedon PC.

Chem Res Toxicol. 2017 Aug 21;30(8):1572-1576. doi: 10.1021/acs.chemrestox.7b00075. Epub 2017 Jul 27.

12.

The m6A pathway facilitates sex determination in Drosophila.

Kan L, Grozhik AV, Vedanayagam J, Patil DP, Pang N, Lim KS, Huang YC, Joseph B, Lin CJ, Despic V, Guo J, Yan D, Kondo S, Deng WM, Dedon PC, Jaffrey SR, Lai EC.

Nat Commun. 2017 Jul 4;8:15737. doi: 10.1038/ncomms15737.

13.

Three distinct 3-methylcytidine (m3C) methyltransferases modify tRNA and mRNA in mice and humans.

Xu L, Liu X, Sheng N, Oo KS, Liang J, Chionh YH, Xu J, Ye F, Gao YG, Dedon PC, Fu XY.

J Biol Chem. 2017 Sep 1;292(35):14695-14703. doi: 10.1074/jbc.M117.798298. Epub 2017 Jun 27.

14.

Structural mimicry of the dengue virus envelope glycoprotein revealed by the crystallographic study of an idiotype-anti-idiotype Fab complex.

Wong YH, Goh BC, Lim SY, Teo EW, Lim APC, Dedon PC, Hanson BJ, MacAry PA, Lescar J.

J Virol. 2017 Jun 21. pii: JVI.00406-17. doi: 10.1128/JVI.00406-17. [Epub ahead of print]

15.

Oxidation of phosphorothioate DNA modifications leads to lethal genomic instability.

Kellner S, DeMott MS, Cheng CP, Russell BS, Cao B, You D, Dedon PC.

Nat Chem Biol. 2017 Aug;13(8):888-894. doi: 10.1038/nchembio.2407. Epub 2017 Jun 12.

16.

Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes.

Chen C, Wang L, Chen S, Wu X, Gu M, Chen X, Jiang S, Wang Y, Deng Z, Dedon PC, Chen S.

Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):4501-4506. doi: 10.1073/pnas.1702450114. Epub 2017 Apr 11.

17.

Production of Superoxide in Bacteria Is Stress- and Cell State-Dependent: A Gating-Optimized Flow Cytometry Method that Minimizes ROS Measurement Artifacts with Fluorescent Dyes.

McBee ME, Chionh YH, Sharaf ML, Ho P, Cai MW, Dedon PC.

Front Microbiol. 2017 Mar 21;8:459. doi: 10.3389/fmicb.2017.00459. eCollection 2017.

18.

tRNA N6-adenosine threonylcarbamoyltransferase defect due to KAE1/TCS3 (OSGEP) mutation manifest by neurodegeneration and renal tubulopathy.

Edvardson S, Prunetti L, Arraf A, Haas D, Bacusmo JM, Hu JF, Ta-Shma A, Dedon PC, de Crécy-Lagard V, Elpeleg O.

Eur J Hum Genet. 2017 May;25(5):545-551. doi: 10.1038/ejhg.2017.30. Epub 2017 Mar 8.

19.

tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence.

Chionh YH, McBee M, Babu IR, Hia F, Lin W, Zhao W, Cao J, Dziergowska A, Malkiewicz A, Begley TJ, Alonso S, Dedon PC.

Nat Commun. 2016 Nov 11;7:13302. doi: 10.1038/ncomms13302.

20.

Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa.

Jaroensuk J, Atichartpongkul S, Chionh YH, Wong YH, Liew CW, McBee ME, Thongdee N, Prestwich EG, DeMott MS, Mongkolsuk S, Dedon PC, Lescar J, Fuangthong M.

Nucleic Acids Res. 2016 Dec 15;44(22):10834-10848. Epub 2016 Sep 28.

21.

N(6)-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis.

Shen L, Liang Z, Gu X, Chen Y, Teo ZW, Hou X, Cai WM, Dedon PC, Liu L, Yu H.

Dev Cell. 2016 Jul 25;38(2):186-200. doi: 10.1016/j.devcel.2016.06.008. Epub 2016 Jul 7.

22.

The role of sequence context, nucleotide pool balance and stress in 2'-deoxynucleotide misincorporation in viral, bacterial and mammalian RNA.

Wang J, Dong H, Chionh YH, McBee ME, Sirirungruang S, Cunningham RP, Shi PY, Dedon PC.

Nucleic Acids Res. 2016 Oct 14;44(18):8962-8975. Epub 2016 Jun 30.

23.

Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress.

Lin W, de Sessions PF, Teoh GH, Mohamed AN, Zhu YO, Koh VH, Ang ML, Dedon PC, Hibberd ML, Alonso S.

Infect Immun. 2016 Aug 19;84(9):2505-23. doi: 10.1128/IAI.00072-16. Print 2016 Sep.

24.

Gene- and genome-based analysis of significant codon patterns in yeast, rat and mice genomes with the CUT Codon UTilization tool.

Doyle F, Leonardi A, Endres L, Tenenbaum SA, Dedon PC, Begley TJ.

Methods. 2016 Sep 1;107:98-109. doi: 10.1016/j.ymeth.2016.05.010. Epub 2016 May 28.

25.

Immunostimulating and Gram-negative-specific antibacterial cyclotides from the butterfly pea (Clitoria ternatea).

Nguyen KN, Nguyen GK, Nguyen PQ, Ang KH, Dedon PC, Tam JP.

FEBS J. 2016 Jun;283(11):2067-90. doi: 10.1111/febs.13720. Epub 2016 Apr 20.

26.

Novel genomic island modifies DNA with 7-deazaguanine derivatives.

Thiaville JJ, Kellner SM, Yuan Y, Hutinet G, Thiaville PC, Jumpathong W, Mohapatra S, Brochier-Armanet C, Letarov AV, Hillebrand R, Malik CK, Rizzo CJ, Dedon PC, de Crécy-Lagard V.

Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):E1452-9. doi: 10.1073/pnas.1518570113. Epub 2016 Feb 29.

27.

Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation.

Deng W, Babu IR, Su D, Yin S, Begley TJ, Dedon PC.

PLoS Genet. 2015 Dec 15;11(12):e1005706. doi: 10.1371/journal.pgen.1005706. eCollection 2015 Dec.

28.

An extensive allelic series of Drosophila kae1 mutants reveals diverse and tissue-specific requirements for t6A biogenesis.

Lin CJ, Smibert P, Zhao X, Hu JF, Ramroop J, Kellner SM, Benton MA, Govind S, Dedon PC, Sternglanz R, Lai EC.

RNA. 2015 Dec;21(12):2103-18. doi: 10.1261/rna.053934.115. Epub 2015 Oct 29.

29.

Metabolic fate of endogenous molecular damage: Urinary glutathione conjugates of DNA-derived base propenals as markers of inflammation.

Jumpathong W, Chan W, Taghizadeh K, Babu IR, Dedon PC.

Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):E4845-53. doi: 10.1073/pnas.1503945112. Epub 2015 Aug 17.

30.

A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications.

Cai WM, Chionh YH, Hia F, Gu C, Kellner S, McBee ME, Ng CS, Pang YL, Prestwich EG, Lim KS, Babu IR, Begley TJ, Dedon PC.

Methods Enzymol. 2015;560:29-71. doi: 10.1016/bs.mie.2015.03.004. Epub 2015 Jul 17.

31.

Alkbh8 Regulates Selenocysteine-Protein Expression to Protect against Reactive Oxygen Species Damage.

Endres L, Begley U, Clark R, Gu C, Dziergowska A, Małkiewicz A, Melendez JA, Dedon PC, Begley TJ.

PLoS One. 2015 Jul 6;10(7):e0131335. doi: 10.1371/journal.pone.0131335. eCollection 2015.

32.

Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses.

Endres L, Dedon PC, Begley TJ.

RNA Biol. 2015;12(6):603-14. doi: 10.1080/15476286.2015.1031947. Review.

33.

Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes.

Chan CT, Deng W, Li F, DeMott MS, Babu IR, Begley TJ, Dedon PC.

Chem Res Toxicol. 2015 May 18;28(5):978-88. doi: 10.1021/acs.chemrestox.5b00004. Epub 2015 Apr 13.

34.
35.

RNA editing, epitranscriptomics, and processing in cancer progression.

Witkin KL, Hanlon SE, Strasburger JA, Coffin JM, Jaffrey SR, Howcroft TK, Dedon PC, Steitz JA, Daschner PJ, Read-Connole E.

Cancer Biol Ther. 2015;16(1):21-7. doi: 10.4161/15384047.2014.987555.

36.

More than an adaptor molecule: the emerging role of tRNA in cell signaling and disease.

Ribas de Pouplana L, Dedon PC.

FEBS Lett. 2014 Nov 28;588(23):4267. No abstract available.

37.

Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number.

Pang YL, Abo R, Levine SS, Dedon PC.

Nucleic Acids Res. 2014 Dec 16;42(22):e170. doi: 10.1093/nar/gku945. Epub 2014 Oct 27.

38.

tRNA modifications regulate translation during cellular stress.

Gu C, Begley TJ, Dedon PC.

FEBS Lett. 2014 Nov 28;588(23):4287-96. doi: 10.1016/j.febslet.2014.09.038. Epub 2014 Oct 7. Review.

39.

Pathological phenotypes and in vivo DNA cleavage by unrestrained activity of a phosphorothioate-based restriction system in Salmonella.

Cao B, Cheng Q, Gu C, Yao F, DeMott MS, Zheng X, Deng Z, Dedon PC, You D.

Mol Microbiol. 2014 Aug;93(4):776-85. doi: 10.1111/mmi.12692. Epub 2014 Jul 23.

40.

Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences.

Cao B, Chen C, DeMott MS, Cheng Q, Clark TA, Xiong X, Zheng X, Butty V, Levine SS, Yuan G, Boitano M, Luong K, Song Y, Zhou X, Deng Z, Turner SW, Korlach J, You D, Wang L, Chen S, Dedon PC.

Nat Commun. 2014 Jun 5;5:3951. doi: 10.1038/ncomms4951.

41.

Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry.

Su D, Chan CT, Gu C, Lim KS, Chionh YH, McBee ME, Russell BS, Babu IR, Begley TJ, Dedon PC.

Nat Protoc. 2014 Apr;9(4):828-41. doi: 10.1038/nprot.2014.047. Epub 2014 Mar 13.

42.

28S rRNA is inducibly pseudouridylated by the mTOR pathway translational control in CHO cell cultures.

Courtes FC, Gu C, Wong NS, Dedon PC, Yap MG, Lee DY.

J Biotechnol. 2014 Mar 20;174:16-21. doi: 10.1016/j.jbiotec.2014.01.024. Epub 2014 Jan 27.

43.

A system of RNA modifications and biased codon use controls cellular stress response at the level of translation.

Dedon PC, Begley TJ.

Chem Res Toxicol. 2014 Mar 17;27(3):330-7. doi: 10.1021/tx400438d. Epub 2014 Jan 27.

44.

Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs.

Mandal D, Köhrer C, Su D, Babu IR, Chan CT, Liu Y, Söll D, Blum P, Kuwahara M, Dedon PC, Rajbhandary UL.

RNA. 2014 Feb;20(2):177-88. doi: 10.1261/rna.042358.113. Epub 2013 Dec 16.

45.

Dosimetry of N⁶-formyllysine adducts following [¹³C²H₂]-formaldehyde exposures in rats.

Edrissi B, Taghizadeh K, Moeller BC, Kracko D, Doyle-Eisele M, Swenberg JA, Dedon PC.

Chem Res Toxicol. 2013 Oct 21;26(10):1421-3. doi: 10.1021/tx400320u. Epub 2013 Oct 10.

46.

Induction of functional human macrophages from bone marrow promonocytes by M-CSF in humanized mice.

Li Y, Chen Q, Zheng D, Yin L, Chionh YH, Wong LH, Tan SQ, Tan TC, Chan JK, Alonso S, Dedon PC, Lim B, Chen J.

J Immunol. 2013 Sep 15;191(6):3192-9. doi: 10.4049/jimmunol.1300742. Epub 2013 Aug 9.

47.

Chemistry meets biology in colitis-associated carcinogenesis.

Mangerich A, Dedon PC, Fox JG, Tannenbaum SR, Wogan GN.

Free Radic Res. 2013 Nov;47(11):958-86. doi: 10.3109/10715762.2013.832239. Epub 2013 Oct 4. Review.

48.

A multidimensional platform for the purification of non-coding RNA species.

Chionh YH, Ho CH, Pruksakorn D, Ramesh Babu I, Ng CS, Hia F, McBee ME, Su D, Pang YL, Gu C, Dong H, Prestwich EG, Shi PY, Preiser PR, Alonso S, Dedon PC.

Nucleic Acids Res. 2013 Sep;41(17):e168. doi: 10.1093/nar/gkt668. Epub 2013 Aug 1.

49.

DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis.

Shell SS, Prestwich EG, Baek SH, Shah RR, Sassetti CM, Dedon PC, Fortune SM.

PLoS Pathog. 2013;9(7):e1003419. doi: 10.1371/journal.ppat.1003419. Epub 2013 Jul 4.

50.

Chemical and cytokine features of innate immunity characterize serum and tissue profiles in inflammatory bowel disease.

Knutson CG, Mangerich A, Zeng Y, Raczynski AR, Liberman RG, Kang P, Ye W, Prestwich EG, Lu K, Wishnok JS, Korzenik JR, Wogan GN, Fox JG, Dedon PC, Tannenbaum SR.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):E2332-41. doi: 10.1073/pnas.1222669110. Epub 2013 Jun 10.

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