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Microbiome and microbiome-host interactions

  • Zhang, W., R-Y. Xu, Z. Matuszek, Z. Cai, Tao Pan*: Detection and quantification of glycosylated queuosine modified tRNAs by acid denaturing and APB gels, RNA 26, 1291-1298 (2020).
  • Zhang, J., Lu, R., Zhang, Y., Matuszek, Z., Zhang, W., Xia, Y., Tao Pan, J. Sun: tRNA queuosine modification enzyme modulates the growth and microbiome recruitment to breast tumors, Cancer, 12, 628 (2020).
  • Wang*, X.Y., Y. Li, W-J. Chen, H-L. Shi, A.M. Eren, A. Morozov, C. He, G-Z. Luo*, Tao Pan*: Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome, Cell Res. 29, 167–170 (2019).
  • Schwartz, M.H., H.P. Wang, J.N. Pan, W.C. Clark, S. Cui, M.J. Eckwahl, D.W. Pan, M. Parisien, S.M. Owens, B.L. Cheng, K. Martinez, J.B. Xu, E.B. Chang, Tao Pan*, A.M. Eren*: Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis, Nature Communications 9:5353, p.1-13 (2018).
  • Wang*, X-W., Z. Matuszek, Y. Huang, M. Parisien, Q. Dai, W.C. Clark, M.H. Schwartz, Tao Pan*: Queuosine modification protects cognate tRNAs against ribonuclease cleavage, RNA 24, 1305-1313 (2018).

tRNA-seq and applications

  • Wang, Y.U., C.D. Katanski, C. Watkins, J.N. Pan, Q. Dai, Z-X. Jiang, Tao Pan*: A High-throughput Screening Method for Evolving a Demethylase Enzyme with Improved and New Functionalities, Nucl. Acids Res., in press (2020).
  • Richter, U., M.E. Evans, W.C. Clark, P. Marttinen, E. Shoubridge, A. Suomalainen, A. Wredenberg, A. Wedell, Tao Pan* & B. Battersby*: RNA modification landscape of the human mitochondrial tRNALys regulates protein synthesis, Nature Communications 9, 3966, p.1-11 (2018).
  • Evans, M.E., W.C. Clark, G-Q. Zheng & Tao Pan*: Determination of tRNA aminoacylation levels by high throughput sequencing, Nucl. Acids Res. 45, e133, p.1-8 (2017).
  • Dai, Q., G-Q. Zheng, M.H. Schwartz, W.C. Clark & Tao Pan*: Selective enzymatic demethylation of N2,N2-dimethylguanosine in RNA and its application in high-throughput tRNA sequencing, Angewandte Chemie (Int) 56, 5017-5020 (2017).
  • Clark, W.C., M.E. Evans, D. Dominissini, G-Q. Zheng, Tao Pan*: tRNA base methylation identification and quantification via high throughput sequencing, RNA 22, 1771-1784 (2016).

mRNA and viral RNA modifications

  • Eckwahl, M., R-Y. Xu, J. Michalkiewicz, W. Zhang, P. Patel, Z. Cai, Tao Pan*: 5-methylcytosine RNA modifications promote retrovirus replication in an ALYREF reader protein-dependent manner, J. Virology 94, e00544-20 (2020).
  • Jurczyszak, D., W. Zhang, S.N. Terry, T. Kehrer, M.C.B. González, E. McGregor, L.C.F. Mulder, M.J. Eckwahl, Tao Pan*, V. Simon*: HIV protease cleaves the antiviral m6A reader protein YTHDF3 in the viral particle, PLoS Pathogens, 16, e1008305 (2020).
  • Zhou, K.I., H-L. Shi, R.T. Lyu, A.C. Wylder, Z. Matuszek, J.N. Pan, C. He, M. Parisien*, Tao Pan*: Regulation of co-transcriptional pre-mRNA splicing by m6A through the low-complexity protein hnRNPG, Mol. Cell 76, 70-81 (2019).
  • Liu, N., K.I. Zhou, M. Parisien, Q. Dai, L. Diatchenko & Tao Pan*: N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein, Nucl. Acids Res. 45, 6051-6063 (2017).
  • Zhou, K.I., N. Liu & Tao Pan*: Identification of N6-methyladenosine reader proteins, Methods 126, 105-111 (2017).
  • Zhou, K.I., M. Parisien, Q. Dai, N. Liu, L. Diatchenko, J.R. Sachleben & Tao Pan*: N6-methyladenosine modification in a long non-coding RNA hairpin predisposes its conformation to protein binding, J. Mol. Biol. 428, 822-33 (2016).
  • Dominissini, D., S. Nachtergaele, S. Moshitch-Moshkovitz, E. Peer, N. Kol, M.S. Ben-Haim, Q. Dai, A. Di Segni, M. Salmon-Divon, W.C. Clark, G.Q. Zheng, Tao Pan, O. Solomon, E. Eyal, V. Hershkovitz, D. Han, L.C. Doré, N. Amariglio, G.Rechavi, C. He: The dynamic N1-methyladenosine (m1A) methylomes in eukaryotic messenger RNA, Nature 530, 441-6 (2016).

Other RNA modifications

  • Zhang, W., M.J. Eckwahl, K.I. Zhou, Tao Pan*: Sensitive and quantitative probing of pseudouridine modification in mRNA and long non-coding RNA, RNA 25, 1218-1225 (2019).
  • Ma, H.H., X.Y. Wang, J.B. Cai, Q. Dai, S. K. Natchiar, R. Lv, K. Chen, Z.K. Lu2, H. Chen, Y.J.G. Shi, F. Lan, J. Fan, B.P. Klaholz, Tao Pan*, Y. Shi*, C. He*: N6-methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation, Nature Chem. Biol. 15, 88–94 (2019).
  • Zhou, K.I., W.C. Clark, D.W. Pan, M.J. Eckwahl, Q. Dai & Tao Pan*: Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing, RNA Biol. 15, 892-900 (2018).
  • Macari, F., Y. El-houfi, G. Bolina, A. Bystöm, S. Khoury-Hanna, J. Ollier, L. Yazdani, G. Zheng, I. Bièche, N. Legrand, L. M’Batchi, S. Durrieu, S. Delbecq, C. Bonnans, B. Lapeyre, L. Bauchet, J. Pannequin, F. Hollande, M. Teichmann, S. Vagner, Tao Pan, A. David, A. Choquet, D. Joubert: TRM6/61 connects PKCα with translational control through tRNAiMet stabilization: impact on tumorigenesis, Oncogene 35, 1785-96 (2016).
  • Liu, F., W. Clark, G-Z. Luo, X-Y. Wang, Y. Fu, J-B. Wei, X. Wang, Z-Y. Hao, Q. Dai, G-Q. Zheng, H-H. Ma, D. Han, M. Evans, A. Klungland, Tao Pan* & C. He*: ALKBH1-Mediated tRNA Demethylation Regulates Translation, Cell 167, 816-828 (2016).

Adaptive mistranslation

  • Schwartz*, M.H., Tao Pan*: Determining the fidelity of tRNA aminoacylation via microarrays, Methods 113, 27-33 (2017).
  • Schwartz*, M.H. & Tao Pan*: tRNA misacylation with methionine in the mouse gut microbiome in situ, Microbial Ecology 74, 10-14 (2017).
  • Schwartz, M.H., J.R. Waldbauer, L-C. Zhang, Tao Pan*: Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli, Nucl. Acids Res. 44, 10292-10303 (2016).
  • Sun, L-T. A.C. Gomes, W-W. He, H-H. Zhou, X-Y. Wang, D.W. Pan, P. Schimmel, Tao Pan* & X-L. Yang*: Evolutionary gain of alanine mischarging to non-cognate tRNAs with a G4:U69 base pair, J. Am. Chem. Soc. 138, 12948-12955 (2016).
  • Gomes, A.C., A.J. Kordala, R. Strack, X-Y. Wang, R. Geslain, K. Delaney, W.C. Clark, R. Keenan, Tao Pan*: A dual fluorescent reporter for the investigation of methionine mistranslation in live cells, RNA 22, 467-76. (2016).
  • Schwartz, M.H. & Tao Pan*: Temperature dependent mistranslation in a hyperthermophile adapts proteins to lower temperatures, Nucl. Acids Res. 44, 294-303 (2016).
  • Wang*, X-Y., Tao Pan*: Methionine Mistranslation Bypasses the Restraint of the Genetic Code to Generate Mutant Proteins with Distinct Activities, PLoS Genetics 11, e1005745, p. 1-20 (2015).

tRNA and tRNA synthetase

  • Sun, L.T., N. Wei, B. Kuhle, D. Blocque, S. Novick, Z. Matuszek, H.H. Zhou, W.W, He, J.J. Zhang, T. Weber, R. Horvath, P. Latour, Tao Pan, P. Schimmel, P. Griffin, X-L. Yang: CMT2N-causing aminoacylation domain mutants enable Nrp1 interaction with AlaRS, Proc. Natl. Acad. Sci. USA, in press (2021).
  • Chen, M-R. B. Kuhle, J. Diedrich, Z. Liu, J.J. Moresco, J.R. Yates III, Tao Pan, X-L. Yang: Trans-editing activity of a tRNA synthetase allows vertebrates to abundantly express mischargeable tRNA without causing mistranslation, Nucl. Acids Res. 48, 6445–6457 (2020).
  • Blocquel, D. L. Sun, Z. Matuszek, S. Li, T. Weber, B. Kuhle, G. Kooi, N. Wei, J. Baets, Tao Pan, P. Schimmel, X-L. Yang: CMT disease severity correlates with mutation-induced open conformation of His-tRNA synthetase, not aminoacylation loss in patient cells, Proc. Natl. Acad. Sci. USA 116, 19440-19448 (2019).
  • Peterlin, B.M., P-Y. Liu, X-Y. Wang, D. Cary, W. Shao, T. Hong, Tao Pan, K. Fujinaga: Hili inhibits HIV replication in activated T cells, J. Virology 91, e00237-17, p. 1-14 (2017).
  • Saikia, M., X-Y. Wang, Y. Mao, J. Wan, Tao Pan & S-B. Qian: Codon optimality controls differential mRNA translation during amino acid starvation, RNA 22, 1719-1727 (2016).
  • Wang, X-Y., C.R. Chow, K. Ebine, J-Y. Lee, M.R. Rosner, Tao Pan* & H.G. Munshi*: Interaction of tRNA with MEK2 in pancreatic cancer cells, Sci. Reports 6, 28260, p. 1-9 (2016).

Reviews and commentaries

  • Zhang, W., Tao Pan*: A dual function PUS enzyme, Nature Chem. Biol., 16, 107-108 (2020). [Commentary]
  • Tao Pan: Modifications and functional genomics of human transfer RNA, Cell Res. 28, 395–404 (2018). [Review]
  • Zhou, K.I., Tao Pan*: An additional class of N6-methyladenosine readers, Nature Cell Biol. 20, 230–232 (2018). [Commentary]
  • Roundtree, I.A., M.E. Evans, Tao Pan*, C. He*: Dynamic RNA modifications in gene expression regulation, Cell 169, 1187-1200 (2017). [Review]
  • Schwartz*, M.H., Tao Pan*: Function and origin of mistranslation in distinct cellular contexts, Crit. Rev. Biochem. Mol. Biol. 52, 205-219 (2017). [Review]
  • Lewis, C.J.T., Tao Pan* & A. Kalsotra*: RNA Modifications and Structures Cooperate to Guide RNA-protein Interactions, Nature Rev. Mol. Cell Biol. 18, 202-210 (2017). [Review]
  • Liu, N. & Tao Pan*: RNA epigenetics (epitranscriptomics). In "Translating epigenetics to the clinic" ed. Laurence, J. & Van Beusekom, M., Academic Press, Elsevier, pp.19-36 (2017). [Review]
  • Zhou, K.I., Tao Pan: Structures of the m6A methyltransferase complex: two subunits with distinct but coordinated roles, Mol. Cell 63, 183-185 (2016). [Preview]
  • Wang, X-Y., Tao Pan: Stress response and adaptation mediated by amino acid misincorporation during protein synthesis, Adv. in Nutrition 7, 773S-779S (2016). [Review]
  • Frye, M., S.R. Jaffrey, Tao Pan, G. Rechavi & T. Suzuki: RNA modifications: what have we learned and where are we headed? Nature Review Genetics 17, 365–372 (2016). [Opinion]
  • Liu, N. & Tao Pan: N6-methyladenosine-coded RNA Epitranscriptomics, Nature Mol. & Struct. Biol. 23, 98-102 (2016). [Review]

Selected older publications

  • Zheng, G.Q., Y. Qin, W.C. Clark, Q. Dai, C.Q. Yi, C. He, A. M. Lambowitz*, Tao Pan*: Efficient and quantitative high-throughput transfer RNA sequencing, Nature Methods 12, 835-837 (2015).
  • Liu, N., Q. Dai, GQ. Zheng, C. He, M. Parisien*, Tao Pan*: N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions, Nature 518, 560-564 (2015).
  • Liu, N. & Tao Pan: RNA epigenetics, Translational Research 165 165, 28-35 (2015). [review]
  • Zaborske, J.M., V. L. DuMont, E. W. J. Wallace, Tao Pan, C. F. Aquadro & D. A. Drummond: A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus, PLoS Biology 13, e1002015, p.1-13 (2014).
  • Parisien, M., X. Wang, Tao Pan*: Diversity of human tRNA genes from the 1,000-genomes project, RNA Biology 10, 1853-1867 (2013).
  • Liu, N., M. Parisien, Q. Dai, G-Q. Zheng, C. He & Tao Pan*: Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long non-coding RNA, RNA 19, 1848-1856 (2013).
  • Tao Pan: Adaptive translation as a mechanism of stress response and adaptation, Ann. Rev. Genetics 47, 139-155 (2013). [review]
  • Parisien, M., X-Y. Wang, G. Perdrizet II, C. Lamphear, C.A. Fierke, K.C. Maheshwari, M.J. Wilde, T.R. Sosnick*, Tao Pan*: Discovering RNA-protein interactome using chemical context profiling of the RNA-protein interface, Cell Reports, 3, 1703-13 (2013).
  • Pavon-Eternod, M., S. Gomes, M.R. Rosner* & Tao Pan*: Overexpression of Initiator Methionine tRNA Leads to Global Reprogramming of tRNA Expression and Increased Proliferation in Human Epithelial Cells, RNA 19, 461-6 (2013).
  • Tao Pan: N6-methyl-Adenosine modification in messenger and long non-coding RNA, Trends in Biochem. Sci. 38, 204-9 (2013). [review]
  • Perdrizet, G.A., I. Artsimovitch, R. Furman, T. R. Sosnick*, Tao Pan*: Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch, Proc. Natl. Acad. Sci. USA 109, 3323-3328 (2012).
  • Zhou, D-H, J-Y. Lee, C. Frankenberger, R. Geslain*, M. Rosner*, Tao Pan*: Anti-tumor effects of an engineered "killer" transfer RNA, Biochem. Biophys. Res. Comm. 427, 148-153 (2012).
  • Jones, T.E., R.W. Alexander, Tao Pan*: Misacylation of specific non-methionyl-tRNAs by a bacterial methionyl-tRNA synthetases, Proc. Natl. Acad. Sci. USA, 108, 6933-6938 (2011).
  • Fu, Y., Q. Dai, W. Zhang, J. Ren, Tao Pan* & C. He*: The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the anticodon wobble base in tRNA, Angewandte Chemie (Int) 49, 8885-8888 (2010).
  • Zaborske, J.M., X-C. Wu, R. C. Wek, Tao Pan*: Selective control of amino acid metabolism by the GCN2 eIF2 kinase pathway in Saccharomyces cerevisiae, BMC Biochemistry 11:e29 (2010).
  • Saikia, M., Y. Fu, M. Pavon-Eternod, C. He & Tao Pan*: Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs, RNA, RNA 16, 1317-1327 (2010).
  • Geslain, R. & Tao Pan*: Functional analysis of human tRNA isodecoders, J. Mol. Biol. 396, 821-831 (2010).
  • Pavon-Eternod, M., M. Wei, Tao Pan* & Lawrence Kleiman*: Profiling non-lysyl tRNAs in HIV-1, RNA 16, 267-273 (2010).
  • Netzer, N., J.M. Goodenbour, A. David, K.A. Dittmar, R.B. Jones, J.R. Schneider, D. Boone, E.M. Eves, M.R. Rosner, J.S. Gibbs, A. Embry, B. Dolan, S. Das, H. Hickman, P. Berglund, J.R. Bennink, J.W. Yewdell*, Tao Pan*: Innate Immune and Chemically Triggered Oxidative Stress Modifies Translational Fidelity, Nature 462, 522-526 (2009).
  • Pavon-Eternod, M., S. Gomes, R. Geslain, Q. Dai, M. R. Rosner* & Tao Pan*: tRNA Over-expression in Breast Cancer and Functional Consequences, Nucl. Acids Res. 37, 7268-7280 (2009).
  • Zaborske, J.M., J. Narasimhan, L. Jiang, S.A. Wek, K.A. Dittmar, F. Freimoser, Tao Pan* & R.C. Wek*: Genome-wide analysis of tRNA charging and activation of the eIF2 kinase Gcn2p, J. Biol. Chem. 284, 25254-25267 (2009).
  • Wong, T., T.R. Sosnick* & Tao Pan*: Folding of non-coding RNAs during transcription facilitated by pausing-induced non-native structures, Proc. Natl. Acad. Sci. USA 104, 17995-18000 (2007).
  • Dittmar, K.A., J.M. Goodenbour & Tao Pan*: Tissue specific differences in human transfer RNA expression. PLoS Genetics 2, 2107-2115 (e221, 2006).
  • Saikia, M., Q. Dai, W.A. Decatur, M.J. Fournier, J.A. Piccirilli* & Tao Pan*: A systematic, ligation based approach to study RNA modifications, RNA 12, 2025-2033 (2006).
  • Goodenbour, J.M. & Tao Pan*: Diversity of tRNA genes in eukaryotes. Nucl. Acids Res. 34, 6137-46 (2006).
  • Tao Pan & T.R. Sosnick: RNA folding during transcription. Ann. Rev. Biophysics and Biomol. Dynamics 35, 161-175 (2006) [Review].
  • Baird NJ, Westhof E, Qin H, Pan T*, Sosnick TR*. Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding. J Mol Biol. 352:712-22 (2005).
  • Dittmar KA, Sorensen MA, Elf J, Ehrenberg M, Tao Pan*. Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO Rep. 6:151-7 (2005).
  • Dittmar KA, Mobley EM, Radek AJ, Tao Pan*. Exploring the regulation of tRNA distribution on the genomic scale. J Mol Biol. 337:31-47 (2004).
  • Fang, X-W., P. Thiyagarajan, T.R. Sosnick* & Tao Pan*: The rate-limiting step in the folding of a large ribozyme without kinetic traps. Proc. Natl. Acad. Sci. USA 99, 8518-8523 (2002).
  • Fang, X-W., B.L. Golden, K. Littrell, V. Shelton, P. Thiyagarajan, Tao Pan* & T.R. Sosnick*: The thermodynamic origin of the stability of a thermophilic ribozyme. Proc. Natl. Acad. Sci. USA 98, 4355-4360 (2001).
  • Tao Pan*, I. Artsimovitch, X-W. Fang, R. Landick & T.R. Sosnick*: Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proc. Natl. Acad. Sci. USA 96, 9545-9550 (1999).
  • Loria, A. & Tao Pan*: Domain structure of the ribozyme from eubacterial ribonuclease P. RNA 2, 551-563 (1996).

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