Pan:Publications

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2013-present:

  • 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., in press (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), in press (2017).
  • 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]
  • Schwartz*, M.H., Tao Pan*: Determining the fidelity of tRNA aminoacylation via microarrays, Methods, 113, 27-33 (2017).
  • 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, in press (2017).
  • Schwartz*, M.H. & Tao Pan*: tRNA misacylation with methionine in the mouse gut microbiome in situ, Microbial Ecology, in press (2017).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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., 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).
  • 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]
  • 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).
  • Liu, N. & Tao Pan: N6-methyladenosine-coded RNA Epitranscriptomics, Nature Mol. & Struct. Biol. 23, 98-102 (2016). [Review]
  • 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).
  • 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).
  • 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).
  • Wang*, X-Y., Tao Pan*: Methionine Mistranslation Bypasses the Restraint of the Genetic Code to Generate Mutant Proteins with Distinct Activities, PLoS Genetics, e1005745, p. 1-20 (2015).
  • Wallace, E.W., J.L. Kear-Scott, E.V. Pilipenko, M.H. Schwartz, P.R. Laskowski, A.E. Rojek, C.D. Katanski, J.A. Riback, M.F. Dion, A. Franks, E.M. Airoldi, Tao Pan, B.A. Budnik, D.A. Drummond: Heat stress triggers formation of reversible, specific, functional aggregates of endogenous proteins in yeast, Cell 162, 1286-1298 (2015).
  • 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).
  • Chen, K., Z-K. Lu, X. Wang, Y. Fu, G-Z. Luo, N. Liu, D. Han, D. Dominissini, Q. Dai, Tao Pan & C. He: High-Resolution N6-Methyladenosine (m6A) Map Using Photo-Crosslinking-Assisted m6A Sequencing, Angewandte Chemie (Int) 54, 1587-90 (2015).
  • Liu, N. & Tao Pan: RNA epigenetics, Translational Research 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 e1002015, p.1-13 (2014).
  • Saikia, M., R. Jobava, M. Parisien, A. Putnam, D. Krokowski, XH. Gao, G. Bo-Jhih, Y. Yuan, E. Jankowsky, Z. Feng, GF. Hu, M. Pusztai-Carey, M. Gorla, N.B. Sepuri, Tao Pan & M. Hatzoglou: Angiogenin-Cleaved tRNA Halves Interact with Cytochrome c Protecting Cells from Apoptosis during Osmotic Stress, Mol. Cell. Biol. 34, 2450-2463 (2014).
  • Wang, X., Z-K. Lu, A. Gomez, G.C. Hon, Y. Yue, D. Han, Y. Fu, M. Parisien, Q. Dai, G-F. Jia, B. Ren, Tao Pan & C. He: N6-methyladenosine-dependent regulation of messenger RNA stability, Nature 505, 117-120 (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).
  • Czech, A., S. Wende, M. Mörl, Tao Pan, & Z. Ignatova: Reversible and Rapid Transfer-RNA Deactivation as a Mechanism of Translational Repression in Stress, PLoS Genetics e1003767, p1-9 (2013).
  • Krokowski, D., J. Han, M. Saikia, M. Majumder, C.L. Yuan, B-J. Guan, E. Bevilacqua, O. Bussolati, S. Bröer, P. Arvan, M. Tchórzewski, R.J. Kaufman, M.D. Snider, M. Puchowicz, C.M. Croniger, S.R. Kimball, Tao Pan, A.E. Koromilas & Maria Hatzoglou: A self-defeating anabolic program leads to β-cell loss in ER stress–induced diabetes, J. Biol. Chem. 288, 17202-13 (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]
  • Vilfan, I.D., Y-C. Tsai, T.A. Clark, J. Wegener, Q. Dai, C-Q. Yi, Tao Pan, S.W. Turner, J. Korlach: Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription, J. Nanobiotech. 11:8, 1-11 (2013).
  • Subramaniam, A.R., Tao Pan & P. Cluzel: Environmental perturbations lift the degeneracy of the genetic code in bacteria, Proc. Natl. Acad. Sci. USA 110, 2419-24 (2013).
  • Pavon-Eternod, M., A. David, K. Dittmar, P. Berglund, Tao Pan, J.R. Bennink & J.W. Yewdell, Viruses select rather than adjust tRNAs to optimize translation, Nucl. Acids Res. 41, 1914-21 (2013).
  • Geslain, R., S. Uddin, H. Liu, H-M. Jiang, K. van Besien, Tao Pan, & A. Wickrema: Distinct functions of erythropoietin and stem cell factor are linked to activation of mTOR kinase signaling pathway in human erythroid progenitors, Cytokine 61, 329-335 (2013).


Selected older publications:

  • 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).


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