Pan:Publications

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2009-2013:

  • 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).
  • 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).
  • Saikia, M., D. Krokowski, B-J. Guan, M. Parisien, P. Ivanov, P. Anderson, Tao Pan & Maria Hatzoglou: Genome wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress, J. Biol. Chem. 287, 42708-42725 (2012).
  • Li, M-Q., E. Kao, X. Gao, H. Sandig, K. Limmer, M. Pavon Eternod, T. Jones, S. Landry, Tao Pan, M.D. Weitzman & M. David: Codon usage-based Inhibition of HIV Protein Synthesis by Human Schlafen 11, Nature 491, 125-8 (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).
  • Wiltrout, E., J.M. Goodenbour, M. Frechin & Tao Pan*: Misacylation of tRNA with Methionine in Saccharomyces cerevisiae, Nucl. Acids Res. 40, 10494-10506 (2012).
  • Starck, S.R., V. Jiang, M. Pavon-Eternod, S. Prasad, B. McCarthy, Tao Pan, N. Shastri: Leucine-tRNA Initiates at CUG Start Codons for Protein Synthesis and Presentation by MHC Class I, Science 336, 1719-1723 (2012).
  • Novoa, E.M., M. Pavon Eternod, Tao Pan & L. Ribas de Pouplana: Two anticodon modifications shaped tRNA gene populations and genome structure in bacteria and eukaryotes, Cell 149, 202-13 (2012).
  • 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).
  • Parisien, M., C-Q. Yi & Tao Pan*: Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons, RNA 18, 355-367 (2012).
  • Geslain, R. & Tao Pan: tRNA: a vast reservoir of RNA molecules with unexpected regulatory function, Proc. Natl. Acad. Sci. 108, 16489-90 (2011) [Commentary].
  • Jia, G-F.,Y. Fu, X. Zhao, Q. Dai, G-Q. Zheng, Y. Yang, C-Q. Yi, T. Lindahl, Tao Pan, Y-G. Yang & C. He: N6-Methyladenosine in Nuclear RNA is a Major Substrate of the Obesity-Associated FTO, Nature Chem. Biol. 7, 885-887 (2011).
  • Yi, C-Q. & Tao Pan: Cellular Dynamics of RNA modification, Acc. Chem. Res. 44, 1380-1388 (2011) [review].
  • 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).
  • Dai, Q., C-X. Song, Tao Pan & C. He: Syntheses of Two 5-Hydroxymethyl-20-deoxycytidine Phosphoramidites with TBDMS as the 5-Hydroxymethyl Protecting Group and Their Incorporation into DNA, J. Org. Chem. 76, 4182-4188 (2011).
  • Baird, N.J., S.J. Ludtke, H. Khant, W. Chiu, Tao Pan* & T.R. Sosnick*: A discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy, J. Am. Chem. Soc. 132, 16352-16353 (2010).
  • Reiter, N.J., Osterman, A., Torres-Larios, A., Swinger, K.K., Tao Pan & Mondragon, A.: Crystal structure of a bacterial ribonuclease P holoenzyme in complex with tRNA, Nature 468, 784-791 (2010).
  • 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).
  • Zaborske, J.M. & Tao Pan: Genome-wide analysis of Aminoacylation (Charging) levels of tRNA Using Microarrays, J. Vis. Exp. 40, doi: 10.3791/2007 (2010) [Method].
  • 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).
  • Tuller, T., A. Carmi, K. Vestsigian, S. Navon, Y. Dorfan, J. Zaborske, Tao Pan, O. Dahan, I. Furman & Y. Pilpel: An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation, Cell 141, 344-354 (2010).
  • Baird, N.J., H-P. Gong, S.S. Zaheer, K.F. Freed, Tao Pan* & T.R. Sosnick*: Extended structures in RNA folding intermediates are due to non-native interactions rather than electrostatic repulsion, J. Mol. Biol. 397, 1298-1306 (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).
  • Wong, T.N. & Tao Pan: RNA Folding during Transcription: Protocols and Studies. Methods in Enzymology 468, 167-193 (2009) [Method].
  • 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).
  • Zhou, Y., J.M. Goodenbour, L.A. Godley, A. Wickrema* & Tao Pan*: High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma, Biochem. Biophys. Res. Comm. 385, 160-164 (2009).
  • Dai, Q., M. Saikia, N-S. Li, Tao Pan* & J.A. Piccirilli*: Efficient Chemical Synthesis of AppDNA by Adenylation of Immobilized DNA-5'-monophosphate, Organic Letters 11, 1067-1070 (2009).


Selected older publications:

  • 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).
  • Torres-Larios A, Swinger KK, Krasilnikov AS, Pan T, Mondragon A. Crystal structure of the RNA component of bacterial ribonuclease P. Nature 437:584-7 (2005).
  • Dittmar KA, Sorensen MA, Elf J, Ehrenberg M, Pan T. Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO Rep. 6:151-7 (2005).
  • Krasilnikov AS, Xiao Y, Pan T, Mondragon A. Basis for structural diversity in homologous RNAs. Science 306:104-7 (2004).
  • Dittmar KA, Mobley EM, Radek AJ, Pan T. Exploring the regulation of tRNA distribution on the genomic scale. J Mol Biol. 337:31-47 (2004).
  • Krasilnikov AS, Yang X, Pan T, Mondragon A. Crystal structure of the specificity domain of ribonuclease P. Nature 421:760-4 (2003).
  • 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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