Loading...
The University of Chicago Header Logo
Keywords
Last Name
Institution

Tao Pan

TitlePROFESSOR
InstitutionUniversity of Chicago
DepartmentBiochem/Mol Bio
AddressChicago IL 60637
Email
vCardDownload vCard

    Collapse Overview 
    Collapse overview
    Our research focuses on (i) functional genomics and biology of tRNA including microbiomes and (ii) epitranscriptomics including microbiome-host interactions.

    tRNA biology: Translational regulation relies on the dynamic properties of tRNA that constantly change to facilitate response and adaptation to new environments and to control gene expression. We developed high throughput sequencing technologies that measure tRNA abundance, charging and modifications in one single sequencing library. We are investigating the roles of tRNA in translational control and extra-translational functions in mammalian cells.

    Microbiome: We also developed tRNA-seq as another approach for microbiome characterization. Standard microbiome characterizations include 16S-seq or shotgun metagenomics. Although powerful, these DNA-based methods do not directly report the microbiome activity such as dynamic gene expression which requires the studies of RNA in the microbiome. Our microbiome tRNA-seq results show extensive variations of tRNA abundance and modification patterns in microbiomes from different sources. We also show that tRNA modification dynamics in the microbiome correlates with tuning the expression of specific microbial proteins, indicating that tRNA-seq can provide new insights in microbiome biology. We are further developing this approach to explore the potentials of tRNA-seq to study microbiomes from humans and from the oceans.

    Epitranscriptomics: Over 100 types of post-transcriptional RNA modifications have been identified in thousands of sites in the transcriptome. They include methylation of bases and the ribose backbone, rotation and reduction of uridine, base deamination, addition of ring structures and carbohydrate moieties, and so on. mRNA modifications are involved in cell differentiation, proliferation, and many other cellular functions and human diseases. Some mRNA modifications can also be removed by cellular enzymes, resulting in the dynamic regulation of their functions. We are investigating the function and mechanisms of mRNA modifications such as N6-methyladenosine (m6A) in the regulation of gene expression. For example, we discovered that m6A modification can alter the local mRNA structure to regulate binding of mRNA binding proteins transcriptome-wide (m6A switch), resulting in changes in mRNA abundance and alternative splicing.

    Microbiome-host interactions through epitranscriptomics: We are working on elucidating the function of mammalian host mRNA and tRNA modifications in response to the gut microbiome. We found that microbiome reprograms the host m6A modifications transcriptome-wide in a tissue-dependent manner, suggesting that this dynamic epitranscriptomic mark is used in yet unknown ways in microbiome response. We also found that a microbiome dependent, host tRNA modification alters the cellular small RNA pool, suggesting yet another pathway of microbiome response through RNA modifications.


    Collapse Biography 
    Collapse education and training
    University des Saarlands, GermanyBS/MS06/1986Chemistry
    Yale University, New Haven, CTPh.D.08/1990Biophysics/Biochemistry
    University of Colorado at Boulder, Boulder, COpostdoctoral12/1993Biochemistry
    Collapse awards and honors
    1991 - 1993Damon Runyon-Walter Winchell Cancer Research Fund
    1994Cancer Research Foundation, Raymond F. Zelko Young Investigator
    1995 - 1997American Cancer Society, Junior Faculty Research Award
    2009 - 2013NIH EUREKA award
    2011 - 2016NIH Director’s Pioneer award
    2015American Association for the Advancement of Science (AAAS) Fellow

    Collapse ORNG Applications 
    Collapse Websites

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Zhang W, Pan T. A dual function PUS enzyme. Nat Chem Biol. 2020 Feb; 16(2):107-108. PMID: 31974524.
      View in: PubMed
    2. Gao X, Guo N, Xu H, Pan T, Lei H, Yan A, Mi Y, Xu L. Ibuprofen induces ferroptosis of glioblastoma cells via downregulation of nuclear factor erythroid 2-related factor 2 signaling pathway. Anticancer Drugs. 2020 Jan; 31(1):27-34. PMID: 31490283.
      View in: PubMed
    3. Zhou Q, Wu X, Wang X, Yu Z, Pan T, Li Z, Chang X, Jin Z, Li J, Zhu Z, Liu B, Su L. The reciprocal interaction between tumor cells and activated fibroblasts mediated by TNF-a/IL-33/ST2L signaling promotes gastric cancer metastasis. Oncogene. 2019 Oct 28. PMID: 31659258.
      View in: PubMed
    4. Blocquel D, Sun L, Matuszek Z, Li S, Weber T, Kuhle B, Kooi G, Wei N, Baets J, Pan T, Schimmel P, Yang XL. CMT disease severity correlates with mutation-induced open conformation of histidyl-tRNA synthetase, not aminoacylation loss, in patient cells. Proc Natl Acad Sci U S A. 2019 Sep 24; 116(39):19440-19448. PMID: 31501329.
      View in: PubMed
    5. Zhou KI, Shi H, Lyu R, Wylder AC, Matuszek Z, Pan JN, He C, Parisien M, Pan T. Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG. Mol Cell. 2019 Oct 03; 76(1):70-81.e9. PMID: 31445886.
      View in: PubMed
    6. Zou G, Chen Q, Chen K, Zuo X, Ge Y, Hou Y, Pan T, Pan H, Liu D, Zhang L, Xiong W. Human Hyperekplexic Mutations in Glycine Receptors Disinhibit the Brainstem by Hijacking GABAA Receptors. iScience. 2019 Sep 27; 19:634-646. PMID: 31450193.
      View in: PubMed
    7. Zhang W, Eckwahl MJ, Zhou KI, Pan T. Sensitive and quantitative probing of pseudouridine modification in mRNA and long noncoding RNA. RNA. 2019 09; 25(9):1218-1225. PMID: 31227565.
      View in: PubMed
    8. Schwartz MH, Wang H, Pan JN, Clark WC, Cui S, Eckwahl MJ, Pan DW, Parisien M, Owens SM, Cheng BL, Martinez K, Xu J, Chang EB, Pan T, Eren AM. Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis. Nat Commun. 2018 12 17; 9(1):5353. PMID: 30559359.
      View in: PubMed
    9. Wang X, Li Y, Chen W, Shi H, Eren AM, Morozov A, He C, Luo GZ, Pan T. Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome. Cell Res. 2019 02; 29(2):167-170. PMID: 30559439.
      View in: PubMed
    10. Ma H, Wang X, Cai J, Dai Q, Natchiar SK, Lv R, Chen K, Lu Z, Chen H, Shi YG, Lan F, Fan J, Klaholz BP, Pan T, Shi Y, He C. N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat Chem Biol. 2019 01; 15(1):88-94. PMID: 30531910.
      View in: PubMed
    11. Richter U, Evans ME, Clark WC, Marttinen P, Shoubridge EA, Suomalainen A, Wredenberg A, Wedell A, Pan T, Battersby BJ. RNA modification landscape of the human mitochondrial tRNALys regulates protein synthesis. Nat Commun. 2018 09 27; 9(1):3966. PMID: 30262910.
      View in: PubMed
    12. Wang X, Matuszek Z, Huang Y, Parisien M, Dai Q, Clark W, Schwartz MH, Pan T. Queuosine modification protects cognate tRNAs against ribonuclease cleavage. RNA. 2018 10; 24(10):1305-1313. PMID: 29970597.
      View in: PubMed
    13. Zhou KI, Clark WC, Pan DW, Eckwahl MJ, Dai Q, Pan T. Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing. RNA Biol. 2018; 15(7):892-900. PMID: 29683381.
      View in: PubMed
    14. Zhou KI, Pan T. An additional class of m6A readers. Nat Cell Biol. 2018 03; 20(3):230-232. PMID: 29476150.
      View in: PubMed
    15. Pan T. Modifications and functional genomics of human transfer RNA. Cell Res. 2018 Apr; 28(4):395-404. PMID: 29463900.
      View in: PubMed
    16. Xu J, Wang Z, Jin X, Li L, Pan T. Methods for Identification of Protein-RNA Interaction. Adv Exp Med Biol. 2018; 1094:117-126. PMID: 30191493.
      View in: PubMed
    17. Evans ME, Clark WC, Zheng G, Pan T. Determination of tRNA aminoacylation levels by high-throughput sequencing. Nucleic Acids Res. 2017 Aug 21; 45(14):e133. PMID: 28586482.
      View in: PubMed
    18. Roundtree IA, Evans ME, Pan T, He C. Dynamic RNA Modifications in Gene Expression Regulation. Cell. 2017 Jun 15; 169(7):1187-1200. PMID: 28622506.
      View in: PubMed
    19. Liu N, Zhou KI, Parisien M, Dai Q, Diatchenko L, Pan T. N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein. Nucleic Acids Res. 2017 Jun 02; 45(10):6051-6063. PMID: 28334903.
      View in: PubMed
    20. Peterlin BM, Liu P, Wang X, Cary D, Shao W, Leoz M, Hong T, Pan T, Fujinaga K. Hili Inhibits HIV Replication in Activated T Cells. J Virol. 2017 06 01; 91(11). PMID: 28331090.
      View in: PubMed
    21. Zhou KI, Liu N, Pan T. Identification of N6-methyladenosine reader proteins. Methods. 2017 08 15; 126:105-111. PMID: 28454774.
      View in: PubMed
    22. Dai Q, Zheng G, Schwartz MH, Clark WC, Pan T. Selective Enzymatic Demethylation of N2 ,N2 -Dimethylguanosine in RNA and Its Application in High-Throughput tRNA Sequencing. Angew Chem Int Ed Engl. 2017 04 24; 56(18):5017-5020. PMID: 28371071.
      View in: PubMed
    23. Lewis CJ, Pan T, Kalsotra A. RNA modifications and structures cooperate to guide RNA-protein interactions. Nat Rev Mol Cell Biol. 2017 03; 18(3):202-210. PMID: 28144031.
      View in: PubMed
    24. Schwartz MH, Pan T. Function and origin of mistranslation in distinct cellular contexts. Crit Rev Biochem Mol Biol. 2017 Apr; 52(2):205-219. PMID: 28075177.
      View in: PubMed
    25. Schwartz MH, Pan T. tRNA Misacylation with Methionine in the Mouse Gut Microbiome in Situ. Microb Ecol. 2017 07; 74(1):10-14. PMID: 28070678.
      View in: PubMed
    26. Liu F, Clark W, Luo G, Wang X, Fu Y, Wei J, Wang X, Hao Z, Dai Q, Zheng G, Ma H, Han D, Evans M, Klungland A, Pan T, He C. ALKBH1-Mediated tRNA Demethylation Regulates Translation. Cell. 2016 Oct 20; 167(3):816-828.e16. PMID: 27745969.
      View in: PubMed
    27. Sun L, Gomes AC, He W, Zhou H, Wang X, Pan DW, Schimmel P, Pan T, Yang XL. Evolutionary Gain of Alanine Mischarging to Noncognate tRNAs with a G4:U69 Base Pair. J Am Chem Soc. 2016 10 05; 138(39):12948-12955. PMID: 27622773.
      View in: PubMed
    28. Schwartz MH, Waldbauer JR, Zhang L, Pan T. Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli. Nucleic Acids Res. 2016 Dec 01; 44(21):10292-10303. PMID: 27672035.
      View in: PubMed
    29. Schwartz MH, Pan T. Determining the fidelity of tRNA aminoacylation via microarrays. Methods. 2017 01 15; 113:27-33. PMID: 27639882.
      View in: PubMed
    30. Saikia M, Wang X, Mao Y, Wan J, Pan T, Qian SB. Codon optimality controls differential mRNA translation during amino acid starvation. RNA. 2016 11; 22(11):1719-1727. PMID: 27613579.
      View in: PubMed
    31. Clark WC, Evans ME, Dominissini D, Zheng G, Pan T. tRNA base methylation identification and quantification via high-throughput sequencing. RNA. 2016 11; 22(11):1771-1784. PMID: 27613580.
      View in: PubMed
    32. Zhou KI, Pan T. Structures of the m(6)A Methyltransferase Complex: Two Subunits with Distinct but Coordinated Roles. Mol Cell. 2016 07 21; 63(2):183-185. PMID: 27447983.
      View in: PubMed
    33. Wang X, Pan T. Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis. Adv Nutr. 2016 07; 7(4):773S-9S. PMID: 27422514.
      View in: PubMed
    34. Wang X, Chow CR, Ebine K, Lee J, Rosner MR, Pan T, Munshi HG. Interaction of tRNA with MEK2 in pancreatic cancer cells. Sci Rep. 2016 06 15; 6:28260. PMID: 27301426.
      View in: PubMed
    35. Frye M, Jaffrey SR, Pan T, Rechavi G, Suzuki T. RNA modifications: what have we learned and where are we headed? Nat Rev Genet. 2016 06; 17(6):365-72. PMID: 27140282.
      View in: PubMed
    36. Dominissini D, Nachtergaele S, Moshitch-Moshkovitz S, Peer E, Kol N, Ben-Haim MS, Dai Q, Di Segni A, Salmon-Divon M, Clark WC, Zheng G, Pan T, Solomon O, Eyal E, Hershkovitz V, Han D, Doré LC, Amariglio N, Rechavi G, He C. The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature. 2016 Feb 25; 530(7591):441-6. PMID: 26863196.
      View in: PubMed
    37. Liu N, Pan T. N6-methyladenosine–encoded epitranscriptomics. Nat Struct Mol Biol. 2016 Feb; 23(2):98-102. PMID: 26840897.
      View in: PubMed
    38. Wang X, Pan T. Correction: Methionine Mistranslation Bypasses the Restraint of the Genetic Code to Generate Mutant Proteins with Distinct Activities. PLoS Genet. 2016 01; 12(1):e1005832. PMID: 26808153.
      View in: PubMed
    39. Gomes AC, Kordala AJ, Strack R, Wang X, Geslain R, Delaney K, Clark WC, Keenan R, Pan T. A dual fluorescent reporter for the investigation of methionine mistranslation in live cells. RNA. 2016 Mar; 22(3):467-76. PMID: 26729921.
      View in: PubMed
    40. Liu N, Pan T. Probing N6-methyladenosine (m6A) RNA Modification in Total RNA with SCARLET. Methods Mol Biol. 2016; 1358:285-92. PMID: 26463390.
      View in: PubMed
    41. Wang X, Pan T. Methionine Mistranslation Bypasses the Restraint of the Genetic Code to Generate Mutant Proteins with Distinct Activities. PLoS Genet. 2015 Dec; 11(12):e1005745. PMID: 26709516.
      View in: PubMed
    42. Schwartz MH, Pan T. Temperature dependent mistranslation in a hyperthermophile adapts proteins to lower temperatures. Nucleic Acids Res. 2016 Jan 08; 44(1):294-303. PMID: 26657639.
      View in: PubMed
    43. Wallace EW, Kear-Scott JL, Pilipenko EV, Schwartz MH, Laskowski PR, Rojek AE, Katanski CD, Riback JA, Dion MF, Franks AM, Airoldi EM, Pan T, Budnik BA, Drummond DA. Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress. Cell. 2015 Sep 10; 162(6):1286-98. PMID: 26359986.
      View in: PubMed
    44. Zhou KI, Parisien M, Dai Q, Liu N, Diatchenko L, Sachleben JR, Pan T. N(6)-Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding. J Mol Biol. 2016 Feb 27; 428(5 Pt A):822-833. PMID: 26343757.
      View in: PubMed
    45. Zheng G, Qin Y, Clark WC, Dai Q, Yi C, He C, Lambowitz AM, Pan T. Efficient and quantitative high-throughput tRNA sequencing. Nat Methods. 2015 Sep; 12(9):835-837. PMID: 26214130.
      View in: PubMed
    46. Liu N, Pan T. Probing RNA Modification Status at Single-Nucleotide Resolution in Total RNA. Methods Enzymol. 2015; 560:149-59. PMID: 26253970.
      View in: PubMed
    47. Pan T. My adventure in tRNA biology, so far. RNA. 2015 Apr; 21(4):707-8. PMID: 25780201.
      View in: PubMed
    48. Liu N, Dai Q, Zheng G, He C, Parisien M, Pan T. N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature. 2015 Feb 26; 518(7540):560-4. PMID: 25719671.
      View in: PubMed
    49. Zaborske JM, DuMont VL, Wallace EW, Pan T, Aquadro CF, Drummond DA. A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus. PLoS Biol. 2014 Dec; 12(12):e1002015. PMID: 25489848.
      View in: PubMed
    50. Chen K, Lu Z, Wang X, Fu Y, Luo GZ, Liu N, Han D, Dominissini D, Dai Q, Pan T, He C. High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing. Angew Chem Int Ed Engl. 2015 Jan 26; 54(5):1587-90. PMID: 25491922.
      View in: PubMed
    51. Saikia M, Jobava R, Parisien M, Putnam A, Krokowski D, Gao XH, Guan BJ, Yuan Y, Jankowsky E, Feng Z, Hu GF, Pusztai-Carey M, Gorla M, Sepuri NB, Pan T, Hatzoglou M. Angiogenin-cleaved tRNA halves interact with cytochrome c, protecting cells from apoptosis during osmotic stress. Mol Cell Biol. 2014 Jul; 34(13):2450-63. PMID: 24752898.
      View in: PubMed
    52. Liu N, Pan T. RNA epigenetics. Transl Res. 2015 Jan; 165(1):28-35. PMID: 24768686.
      View in: PubMed
    53. Parisien M, Wang X, Pan T. Diversity of human tRNA genes from the 1000-genomes project. RNA Biol. 2013 Dec; 10(12):1853-67. PMID: 24448271.
      View in: PubMed
    54. Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M, Dai Q, Jia G, Ren B, Pan T, He C. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014 Jan 02; 505(7481):117-20. PMID: 24284625.
      View in: PubMed
    55. Liu N, Parisien M, Dai Q, Zheng G, He C, Pan T. Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. RNA. 2013 Dec; 19(12):1848-56. PMID: 24141618.
      View in: PubMed
    56. Czech A, Wende S, Mörl M, Pan T, Ignatova Z. Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress. PLoS Genet. 2013 Aug; 9(8):e1003767. PMID: 24009533.
      View in: PubMed
    57. Pan T. Adaptive translation as a mechanism of stress response and adaptation. Annu Rev Genet. 2013; 47:121-37. PMID: 23988117.
      View in: PubMed
    58. Parisien M, Wang X, Perdrizet G, Lamphear C, Fierke CA, Maheshwari KC, Wilde MJ, Sosnick TR, Pan T. Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface. Cell Rep. 2013 May 30; 3(5):1703-13. PMID: 23665222.
      View in: PubMed
    59. Krokowski D, Han J, Saikia M, Majumder M, Yuan CL, Guan BJ, Bevilacqua E, Bussolati O, Bröer S, Arvan P, Tchórzewski M, Snider MD, Puchowicz M, Croniger CM, Kimball SR, Pan T, Koromilas AE, Kaufman RJ, Hatzoglou M. A self-defeating anabolic program leads to ß-cell apoptosis in endoplasmic reticulum stress-induced diabetes via regulation of amino acid flux. J Biol Chem. 2013 Jun 14; 288(24):17202-13. PMID: 23645676.
      View in: PubMed
    60. Vilfan ID, Tsai YC, Clark TA, Wegener J, Dai Q, Yi C, Pan T, Turner SW, Korlach J. Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J Nanobiotechnology. 2013 Apr 03; 11:8. PMID: 23552456.
      View in: PubMed
    61. Pavon-Eternod M, Gomes S, Rosner MR, Pan T. Overexpression of initiator methionine tRNA leads to global reprogramming of tRNA expression and increased proliferation in human epithelial cells. RNA. 2013 Apr; 19(4):461-6. PMID: 23431330.
      View in: PubMed
    62. Pan T. N6-methyl-adenosine modification in messenger and long non-coding RNA. Trends Biochem Sci. 2013 Apr; 38(4):204-9. PMID: 23337769.
      View in: PubMed
    63. Subramaniam AR, Pan T, Cluzel P. Environmental perturbations lift the degeneracy of the genetic code to regulate protein levels in bacteria. Proc Natl Acad Sci U S A. 2013 Feb 05; 110(6):2419-24. PMID: 23277573.
      View in: PubMed
    64. Pavon-Eternod M, David A, Dittmar K, Berglund P, Pan T, Bennink JR, Yewdell JW. Vaccinia and influenza A viruses select rather than adjust tRNAs to optimize translation. Nucleic Acids Res. 2013 Feb 01; 41(3):1914-21. PMID: 23254333.
      View in: PubMed
    65. Geslain R, Uddin S, Liu H, Jiang H, van Besien K, Pan T, Wickrema A. Distinct functions of erythropoietin and stem cell factor are linked to activation of mTOR kinase signaling pathway in human erythroid progenitors. Cytokine. 2013 Jan; 61(1):329-35. PMID: 23148990.
      View in: PubMed
    66. Saikia M, Krokowski D, Guan BJ, Ivanov P, Parisien M, Hu GF, Anderson P, Pan T, Hatzoglou M. Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress. J Biol Chem. 2012 Dec 14; 287(51):42708-25. PMID: 23086926.
      View in: PubMed
    67. Li M, Kao E, Gao X, Sandig H, Limmer K, Pavon-Eternod M, Jones TE, Landry S, Pan T, Weitzman MD, David M. Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11. Nature. 2012 Nov 01; 491(7422):125-8. PMID: 23000900.
      View in: PubMed
    68. Zhou DH, Lee J, Frankenberger C, Geslain R, Rosner M, Pan T. Anti-tumor effects of an engineered "killer" transfer RNA. Biochem Biophys Res Commun. 2012 Oct 12; 427(1):148-53. PMID: 22989754.
      View in: PubMed
    69. Wiltrout E, Goodenbour JM, Fréchin M, Pan T. Misacylation of tRNA with methionine in Saccharomyces cerevisiae. Nucleic Acids Res. 2012 Nov 01; 40(20):10494-506. PMID: 22941646.
      View in: PubMed
    70. Starck SR, Jiang V, Pavon-Eternod M, Prasad S, McCarthy B, Pan T, Shastri N. Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I. Science. 2012 Jun 29; 336(6089):1719-23. PMID: 22745432.
      View in: PubMed
    71. Novoa EM, Pavon-Eternod M, Pan T, Ribas de Pouplana L. A role for tRNA modifications in genome structure and codon usage. Cell. 2012 Mar 30; 149(1):202-13. PMID: 22464330.
      View in: PubMed
    72. Perdrizet GA, Artsimovitch I, Furman R, Sosnick TR, Pan T. Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch. Proc Natl Acad Sci U S A. 2012 Feb 28; 109(9):3323-8. PMID: 22331895.
      View in: PubMed
    73. Parisien M, Yi C, Pan T. Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons. RNA. 2012 Mar; 18(3):355-67. PMID: 22282339.
      View in: PubMed
    74. Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, Yi C, Lindahl T, Pan T, Yang YG, He C. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol. 2011 Oct 16; 7(12):885-7. PMID: 22002720.
      View in: PubMed
    75. Geslain R, Pan T. tRNA: Vast reservoir of RNA molecules with unexpected regulatory function. Proc Natl Acad Sci U S A. 2011 Oct 04; 108(40):16489-90. PMID: 21933958.
      View in: PubMed
    76. Yi C, Pan T. Cellular dynamics of RNA modification. Acc Chem Res. 2011 Dec 20; 44(12):1380-8. PMID: 21615108.
      View in: PubMed
    77. Dai Q, Song CX, Pan T, He C. Syntheses of two 5-hydroxymethyl-2'-deoxycytidine phosphoramidites with TBDMS as the 5-hydroxymethyl protecting group and their incorporation into DNA. J Org Chem. 2011 May 20; 76(10):4182-8. PMID: 21462947.
      View in: PubMed
    78. Jones TE, Alexander RW, Pan T. Misacylation of specific nonmethionyl tRNAs by a bacterial methionyl-tRNA synthetase. Proc Natl Acad Sci U S A. 2011 Apr 26; 108(17):6933-8. PMID: 21482813.
      View in: PubMed
    79. Fu Y, Dai Q, Zhang W, Ren J, Pan T, He C. The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position of tRNA. Angew Chem Int Ed Engl. 2010 Nov 15; 49(47):8885-8. PMID: 20583019.
      View in: PubMed
    80. Reiter NJ, Osterman A, Torres-Larios A, Swinger KK, Pan T, Mondragón A. Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature. 2010 Dec 09; 468(7325):784-9. PMID: 21076397.
      View in: PubMed
    81. Baird NJ, Ludtke SJ, Khant H, Chiu W, Pan T, Sosnick TR. Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy. J Am Chem Soc. 2010 Nov 24; 132(46):16352-3. PMID: 21038867.
      View in: PubMed
    82. Zaborske JM, Wu X, Wek RC, Pan T. Selective control of amino acid metabolism by the GCN2 eIF2 kinase pathway in Saccharomyces cerevisiae. BMC Biochem. 2010 Aug 04; 11:29. PMID: 20684782.
      View in: PubMed
    83. Zaborske J, Pan T. Genome-wide analysis of aminoacylation (charging) levels of tRNA using microarrays. J Vis Exp. 2010 Jun 18; (40). PMID: 20567214.
      View in: PubMed
    84. Saikia M, Fu Y, Pavon-Eternod M, He C, Pan T. Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs. RNA. 2010 Jul; 16(7):1317-27. PMID: 20484468.
      View in: PubMed
    85. Tuller T, Carmi A, Vestsigian K, Navon S, Dorfan Y, Zaborske J, Pan T, Dahan O, Furman I, Pilpel Y. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell. 2010 Apr 16; 141(2):344-54. PMID: 20403328.
      View in: PubMed
    86. Staschke KA, Dey S, Zaborske JM, Palam LR, McClintick JN, Pan T, Edenberg HJ, Wek RC. Integration of general amino acid control and target of rapamycin (TOR) regulatory pathways in nitrogen assimilation in yeast. J Biol Chem. 2010 May 28; 285(22):16893-911. PMID: 20233714.
      View in: PubMed
    87. Baird NJ, Gong H, Zaheer SS, Freed KF, Pan T, Sosnick TR. Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion. J Mol Biol. 2010 Apr 16; 397(5):1298-306. PMID: 20188108.
      View in: PubMed
    88. Geslain R, Pan T. Functional analysis of human tRNA isodecoders. J Mol Biol. 2010 Feb 26; 396(3):821-31. PMID: 20026070.
      View in: PubMed
    89. Pavon-Eternod M, Wei M, Pan T, Kleiman L. Profiling non-lysyl tRNAs in HIV-1. RNA. 2010 Feb; 16(2):267-73. PMID: 20007329.
      View in: PubMed
    90. Netzer N, Goodenbour JM, David A, Dittmar KA, Jones RB, Schneider JR, Boone D, Eves EM, Rosner MR, Gibbs JS, Embry A, Dolan B, Das S, Hickman HD, Berglund P, Bennink JR, Yewdell JW, Pan T. Innate immune and chemically triggered oxidative stress modifies translational fidelity. Nature. 2009 Nov 26; 462(7272):522-6. PMID: 19940929.
      View in: PubMed
    91. Pavon-Eternod M, Gomes S, Geslain R, Dai Q, Rosner MR, Pan T. tRNA over-expression in breast cancer and functional consequences. Nucleic Acids Res. 2009 Nov; 37(21):7268-80. PMID: 19783824.
      View in: PubMed
    92. Zaborske JM, Narasimhan J, Jiang L, Wek SA, Dittmar KA, Freimoser F, Pan T, Wek RC. Genome-wide analysis of tRNA charging and activation of the eIF2 kinase Gcn2p. J Biol Chem. 2009 Sep 11; 284(37):25254-67. PMID: 19546227.
      View in: PubMed
    93. Zhou Y, Goodenbour JM, Godley LA, Wickrema A, Pan T. High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma. Biochem Biophys Res Commun. 2009 Jul 24; 385(2):160-4. PMID: 19450555.
      View in: PubMed
    94. Dai Q, Saikia M, Li NS, Pan T, Piccirilli JA. Efficient chemical synthesis of AppDNA by adenylation of immobilized DNA-5'-monophosphate. Org Lett. 2009 Mar 05; 11(5):1067-70. PMID: 19191584.
      View in: PubMed
    95. Wong TN, Pan T. RNA folding during transcription: protocols and studies. Methods Enzymol. 2009; 468:167-93. PMID: 20946770.
      View in: PubMed
    96. Qu X, Smith GJ, Lee KT, Sosnick TR, Pan T, Scherer NF. Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA. Proc Natl Acad Sci U S A. 2008 May 06; 105(18):6602-7. PMID: 18448679.
      View in: PubMed
    97. Smith GJ, Lee KT, Qu X, Xie Z, Pesic J, Sosnick TR, Pan T, Scherer NF. A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics. J Mol Biol. 2008 May 09; 378(4):943-53. PMID: 18402978.
      View in: PubMed
    98. Wong TN, Sosnick TR, Pan T. Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proc Natl Acad Sci U S A. 2007 Nov 13; 104(46):17995-8000. PMID: 17986617.
      View in: PubMed
    99. Baird NJ, Fang XW, Srividya N, Pan T, Sosnick TR. Folding of a universal ribozyme: the ribonuclease P RNA. Q Rev Biophys. 2007 May; 40(2):113-61. PMID: 17931443.
      View in: PubMed
    100. Dai Q, Fong R, Saikia M, Stephenson D, Yu YT, Pan T, Piccirilli JA. Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine. Nucleic Acids Res. 2007; 35(18):6322-9. PMID: 17881375.
      View in: PubMed
    101. Song XY, Yuan XM, Chen WJ, Pan T, Xie SD, Qin C, Lou C, Jin M, Wang LB, Wu JM. Different criteria for radioactive sentinel lymph nodes has different impact on sentinel node biopsy in breast cancer patients. J Surg Oncol. 2007 Jun 15; 95(8):635-9. PMID: 17252554.
      View in: PubMed
    102. Dittmar KA, Goodenbour JM, Pan T. Tissue-specific differences in human transfer RNA expression. PLoS Genet. 2006 Dec; 2(12):e221. PMID: 17194224.
      View in: PubMed
    103. Goodenbour JM, Pan T. Diversity of tRNA genes in eukaryotes. Nucleic Acids Res. 2006; 34(21):6137-46. PMID: 17088292.
      View in: PubMed
    104. Saikia M, Dai Q, Decatur WA, Fournier MJ, Piccirilli JA, Pan T. A systematic, ligation-based approach to study RNA modifications. RNA. 2006 Nov; 12(11):2025-33. PMID: 16963711.
      View in: PubMed
    105. Torres-Larios A, Swinger KK, Pan T, Mondragón A. Structure of ribonuclease P--a universal ribozyme. Curr Opin Struct Biol. 2006 Jun; 16(3):327-35. PMID: 16650980.
      View in: PubMed
    106. Baird NJ, Srividya N, Krasilnikov AS, Mondragón A, Sosnick TR, Pan T. Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium. RNA. 2006 Apr; 12(4):598-606. PMID: 16581805.
      View in: PubMed
    107. Pan T, Sosnick T. RNA folding during transcription. Annu Rev Biophys Biomol Struct. 2006; 35:161-75. PMID: 16689632.
      View in: PubMed
    108. 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. 2005 Sep 23; 352(3):712-22. PMID: 16115647.
      View in: PubMed
    109. Torres-Larios A, Swinger KK, Krasilnikov AS, Pan T, Mondragón A. Crystal structure of the RNA component of bacterial ribonuclease P. Nature. 2005 Sep 22; 437(7058):584-7. PMID: 16113684.
      View in: PubMed
    110. Le TT, Harlepp S, Guet CC, Dittmar K, Emonet T, Pan T, Cluzel P. Real-time RNA profiling within a single bacterium. Proc Natl Acad Sci U S A. 2005 Jun 28; 102(26):9160-4. PMID: 15967986.
      View in: PubMed
    111. Wong T, Sosnick TR, Pan T. Mechanistic insights on the folding of a large ribozyme during transcription. Biochemistry. 2005 May 24; 44(20):7535-42. PMID: 15895996.
      View in: PubMed
    112. Dittmar KA, Sørensen MA, Elf J, Ehrenberg M, Pan T. Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO Rep. 2005 Feb; 6(2):151-7. PMID: 15678157.
      View in: PubMed
    113. Smith GJ, Sosnick TR, Scherer NF, Pan T. Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization. RNA. 2005 Feb; 11(2):234-9. PMID: 15613536.
      View in: PubMed
    114. Sosnick TR, Pan T. Reduced contact order and RNA folding rates. J Mol Biol. 2004 Oct 01; 342(5):1359-65. PMID: 15364565.
      View in: PubMed
    115. Krasilnikov AS, Xiao Y, Pan T, Mondragón A. Basis for structural diversity in homologous RNAs. Science. 2004 Oct 01; 306(5693):104-7. PMID: 15459389.
      View in: PubMed
    116. Dittmar KA, Mobley EM, Radek AJ, Pan T. Exploring the regulation of tRNA distribution on the genomic scale. J Mol Biol. 2004 Mar 12; 337(1):31-47. PMID: 15001350.
      View in: PubMed
    117. Barrera A, Pan T. Interaction of the Bacillus subtilis RNase P with the 30S ribosomal subunit. RNA. 2004 Mar; 10(3):482-92. PMID: 14970393.
      View in: PubMed
    118. Wang L, Shen J, Song X, Chen W, Pan T, Zhang W, Sun X, He C, Wu J. A study of the lengthening and contractility of the surgical margins in digestive tract cancer. Am J Surg. 2004 Mar; 187(3):452-5. PMID: 15006583.
      View in: PubMed
    119. Song X, Wang L, Chen W, Pan T, Zhu H, Xu J, Jin M, Finley RK, Wu J. Lymphatic mapping and sentinel node biopsy in gastric cancer. Am J Surg. 2004 Feb; 187(2):270-3. PMID: 14769318.
      View in: PubMed
    120. Xie Z, Srividya N, Sosnick TR, Pan T, Scherer NF. Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme. Proc Natl Acad Sci U S A. 2004 Jan 13; 101(2):534-9. PMID: 14704266.
      View in: PubMed
    121. Fang XW, Srividya N, Golden BL, Sosnick TR, Pan T. Stepwise conversion of a mesophilic to a thermophilic ribozyme. J Mol Biol. 2003 Jul 04; 330(2):177-83. PMID: 12823959.
      View in: PubMed
    122. Sosnick TR, Pan T. RNA folding: models and perspectives. Curr Opin Struct Biol. 2003 Jun; 13(3):309-16. PMID: 12831881.
      View in: PubMed
    123. Krasilnikov AS, Yang X, Pan T, Mondragón A. Crystal structure of the specificity domain of ribonuclease P. Nature. 2003 Feb 13; 421(6924):760-4. PMID: 12610630.
      View in: PubMed
    124. Sosnick TR, Pan T. Getting hotter with RNA. Nat Struct Biol. 2002 Nov; 9(11):795-6. PMID: 12402034.
      View in: PubMed
    125. Barrera A, Fang X, Jacob J, Casey E, Thiyagarajan P, Pan T. Dimeric and monomeric Bacillus subtilis RNase P holoenzyme in the absence and presence of pre-tRNA substrates. Biochemistry. 2002 Oct 29; 41(43):12986-94. PMID: 12390025.
      View in: PubMed
    126. Fang XW, Thiyagarajan P, Sosnick TR, Pan T. The rate-limiting step in the folding of a large ribozyme without kinetic traps. Proc Natl Acad Sci U S A. 2002 Jun 25; 99(13):8518-23. PMID: 12084911.
      View in: PubMed
    127. Wang L, Song X, Chen W, Pan T, Zhang W, Sun X, He C, Wu J. [The extensibility and retractility of surgical margins in digestive tract cancer]. Zhonghua Wai Ke Za Zhi. 2002 Apr; 40(4):271-3. PMID: 12133357.
      View in: PubMed
    128. Qin H, Sosnick TR, Pan T. Modular construction of a tertiary RNA structure: the specificity domain of the Bacillus subtilis RNase P RNA. Biochemistry. 2001 Sep 18; 40(37):11202-10. PMID: 11551219.
      View in: PubMed
    129. Loria A, Pan T. Modular construction for function of a ribonucleoprotein enzyme: the catalytic domain of Bacillus subtilis RNase P complexed with B. subtilis RNase P protein. Nucleic Acids Res. 2001 May 01; 29(9):1892-7. PMID: 11328872.
      View in: PubMed
    130. Pan T. Probing RNA structure by lead cleavage. Curr Protoc Nucleic Acid Chem. 2001 May; Chapter 6:Unit 6.3. PMID: 18428864.
      View in: PubMed
    131. Fang XW, Golden BL, Littrell K, Shelton V, Thiyagarajan P, Pan T, Sosnick TR. The thermodynamic origin of the stability of a thermophilic ribozyme. Proc Natl Acad Sci U S A. 2001 Apr 10; 98(8):4355-60. PMID: 11296284.
      View in: PubMed
    132. Shelton VM, Sosnick TR, Pan T. Altering the intermediate in the equilibrium folding of unmodified yeast tRNAPhe with monovalent and divalent cations. Biochemistry. 2001 Mar 27; 40(12):3629-38. PMID: 11297430.
      View in: PubMed
    133. Fang XW, Yang XJ, Littrell K, Niranjanakumari S, Thiyagarajan P, Fierke CA, Sosnick TR, Pan T. The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits. RNA. 2001 Feb; 7(2):233-41. PMID: 11233980.
      View in: PubMed
    134. Loria A, Pan T. The 3' substrate determinants for the catalytic efficiency of the Bacillus subtilis RNase P holoenzyme suggest autolytic processing of the RNase P RNA in vivo. RNA. 2000 Oct; 6(10):1413-22. PMID: 11073217.
      View in: PubMed
    135. Fang X, Littrell K, Yang XJ, Henderson SJ, Siefert S, Thiyagarajan P, Pan T, Sosnick TR. Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering. Biochemistry. 2000 Sep 12; 39(36):11107-13. PMID: 10998249.
      View in: PubMed
    136. Pan T. Probing RNA structure and function, by circular permutation. Methods Enzymol. 2000; 317:313-30. PMID: 10829288.
      View in: PubMed
    137. Fang X, Pan T, Sosnick TR. A thermodynamic framework and cooperativity in the tertiary folding of a Mg2+-dependent ribozyme. Biochemistry. 1999 Dec 21; 38(51):16840-6. PMID: 10606517.
      View in: PubMed
    138. Shelton VM, Sosnick TR, Pan T. Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding. Biochemistry. 1999 Dec 21; 38(51):16831-9. PMID: 10606516.
      View in: PubMed
    139. Fang XW, Pan T, Sosnick TR. Mg2+-dependent folding of a large ribozyme without kinetic traps. Nat Struct Biol. 1999 Dec; 6(12):1091-5. PMID: 10581546.
      View in: PubMed
    140. Mobley EM, Pan T. Design and isolation of ribozyme-substrate pairs using RNase P-based ribozymes containing altered substrate binding sites. Nucleic Acids Res. 1999 Nov 01; 27(21):4298-304. PMID: 10518624.
      View in: PubMed
    141. Pan T, Artsimovitch I, Fang XW, Landick R, Sosnick TR. Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proc Natl Acad Sci U S A. 1999 Aug 17; 96(17):9545-50. PMID: 10449729.
      View in: PubMed
    142. Loria A, Pan T. The cleavage step of ribonuclease P catalysis is determined by ribozyme-substrate interactions both distal and proximal to the cleavage site. Biochemistry. 1999 Jul 06; 38(27):8612-20. PMID: 10393536.
      View in: PubMed
    143. Pan T, Fang X, Sosnick T. Pathway modulation, circular permutation and rapid RNA folding under kinetic control. J Mol Biol. 1999 Feb 26; 286(3):721-31. PMID: 10024446.
      View in: PubMed
    144. Loria A, Niranjanakumari S, Fierke CA, Pan T. Recognition of a pre-tRNA substrate by the Bacillus subtilis RNase P holoenzyme. Biochemistry. 1998 Nov 03; 37(44):15466-73. PMID: 9799509.
      View in: PubMed
    145. Odell L, Huang V, Jakacka M, Pan T. Interaction of structural modules in substrate binding by the ribozyme from Bacillus subtilis RNase P. Nucleic Acids Res. 1998 Aug 15; 26(16):3717-23. PMID: 9685487.
      View in: PubMed
    146. Loria A, Pan T. Recognition of the 5' leader and the acceptor stem of a pre-tRNA substrate by the ribozyme from Bacillus subtilis RNase P. Biochemistry. 1998 Jul 14; 37(28):10126-33. PMID: 9665718.
      View in: PubMed
    147. Pan T, Sosnick TR. Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity. Nat Struct Biol. 1997 Nov; 4(11):931-8. PMID: 9360610.
      View in: PubMed
    148. Pan T. Novel and variant ribozymes obtained through in vitro selection. Curr Opin Chem Biol. 1997 Jun; 1(1):17-25. PMID: 9667827.
      View in: PubMed
    149. Loria A, Pan T. Recognition of the T stem-loop of a pre-tRNA substrate by the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry. 1997 May 27; 36(21):6317-25. PMID: 9174346.
      View in: PubMed
    150. Loria A, Pan T. Domain structure of the ribozyme from eubacterial ribonuclease P. RNA. 1996 Jun; 2(6):551-63. PMID: 8718684.
      View in: PubMed
    151. Pan T, Jakacka M. Multiple substrate binding sites in the ribozyme from Bacillus subtilis RNase P. EMBO J. 1996 May 01; 15(9):2249-55. PMID: 8641290.
      View in: PubMed
    152. Pan T, Loria A, Zhong K. Probing of tertiary interactions in RNA: 2'-hydroxyl-base contacts between the RNase P RNA and pre-tRNA. Proc Natl Acad Sci U S A. 1995 Dec 19; 92(26):12510-4. PMID: 8618931.
      View in: PubMed
    153. Pan T. Novel RNA substrates for the ribozyme from Bacillus subtilis ribonuclease P identified by in vitro selection. Biochemistry. 1995 Jul 04; 34(26):8458-64. PMID: 7541243.
      View in: PubMed
    154. Pan T. Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry. 1995 Jan 24; 34(3):902-9. PMID: 7827048.
      View in: PubMed
    155. Pan T, Zhong K. Selection of circularly permuted ribozymes from Bacillus subtilis RNAse P by substrate binding. Biochemistry. 1994 Nov 29; 33(47):14207-12. PMID: 7524672.
      View in: PubMed
    Pan's Networks
    Click the "See All" links for more information and interactive visualizations!
    Concepts Expand Description
    _
    Co-Authors Expand Description
    _
    Similar People Expand Description
    _
    Same Department Expand Description
    Physical Neighbors Expand Description
    _