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  4. Tao Pan

Tao Pan

Professor
taopan@uchicago.edu
Research Summary
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.
Keywords
Functional genomics, Microbiome, epitranscriptomics, RNA modification, tRNA
Education
  • University des Saarlands, Germany, BS/MS Chemistry 06/1986
  • Yale University, New Haven, CT, Ph.D. Biophysics/Biochemistry 08/1990
  • University of Colorado at Boulder, Boulder, CO, postdoctoral Biochemistry 12/1993
Biosciences Graduate Program Association
Awards & Honors
  • 1991 - 1993 Damon Runyon-Walter Winchell Cancer Research Fund
  • 1994 - Cancer Research Foundation, Raymond F. Zelko Young Investigator
  • 1995 - 1997 American Cancer Society, Junior Faculty Research Award
  • 2009 - 2013 NIH EUREKA award
  • 2011 - 2016 NIH Director’s Pioneer award
  • 2015 - American Association for the Advancement of Science (AAAS) Fellow
Publications

  1. Characteristics of the Northern Hemisphere cold regions changes from 1901 to 2019. Sci Rep. 2023 Mar 08; 13(1):3879. View in: PubMed

  2. [Surgical issues and managements in cochlear reimplantation in 32 children]. Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi. 2023 Mar; 37(3):218-221. View in: PubMed

  3. Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution. Sci Adv. 2023 02 22; 9(8):eabq4632. View in: PubMed

  4. Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation. Nucleic Acids Res. 2023 02 22; 51(3):e17. View in: PubMed

  5. Validation of the Chinese Translation of the "Meaning of Life" in Patients with Hearing Loss or Tinnitus. J Am Acad Audiol. 2022 Dec 10. View in: PubMed

  6. Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications. Mil Med Res. 2022 12 02; 9(1):68. View in: PubMed

  7. tRNA abundance, modification and fragmentation in nasopharyngeal swabs as biomarkers for COVID-19 severity. Front Cell Dev Biol. 2022; 10:999351. View in: PubMed

  8. DKK1 as a robust predictor for adjuvant platinum chemotherapy benefit in resectable pStage II-III gastric cancer. Transl Oncol. 2023 Jan; 27:101577. View in: PubMed

  9. Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution. Nat Biotechnol. 2023 Mar; 41(3):344-354. View in: PubMed

  10. Epitranscriptome profiling of spleen mRNA m6A methylation reveals pathways of host responses to malaria parasite infection. Front Immunol. 2022; 13:998756. View in: PubMed

  11. Age-related endoplasmic reticulum stress represses testosterone synthesis via attenuation of the circadian clock in Leydig cells. Theriogenology. 2022 Sep 01; 189:137-149. View in: PubMed

  12. Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing. Nucleic Acids Res. 2022 09 23; 50(17):e99. View in: PubMed

  13. A multiplex platform for small RNA sequencing elucidates multifaceted tRNA stress response and translational regulation. Nat Commun. 2022 05 05; 13(1):2491. View in: PubMed

  14. The Role of the P1 Latency in Auditory and Speech Performance Evaluation in Cochlear Implanted Children. Neural Plast. 2022; 2022:6894794. View in: PubMed

  15. Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations. Front Cell Dev Biol. 2022; 10:768356. View in: PubMed

  16. Long non-coding RNA ZNF674-AS1 regulates miR-23a/E-cadherin axis to suppress the migration and invasion of non-small cell lung cancer cells. Transl Cancer Res. 2021 Sep; 10(9):4116-4124. View in: PubMed

  17. Pan-cancer assessment of mutational landscape in intrinsically disordered hotspots reveals potential driver genes. Nucleic Acids Res. 2022 05 20; 50(9):e49. View in: PubMed

  18. tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes. Mol Cell. 2022 03 03; 82(5):891-906. View in: PubMed

  19. Clinical impact of Fn-induced high expression of KIR2DL1 in CD8 T lymphocytes in oesophageal squamous cell carcinoma. Ann Med. 2022 Dec; 54(1):51-62. View in: PubMed

  20. [Postoperative hearing in tympanoplasty preserving the manubrium of malleus and tensor tympani muscle tendon]. Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi. 2021 Nov; 35(11):981-987. View in: PubMed

  21. Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling. Genome Biol. 2021 12 06; 22(1):330. View in: PubMed

  22. ImmReg: the regulon atlas of immune-related pathways across cancer types. Nucleic Acids Res. 2021 12 02; 49(21):12106-12118. View in: PubMed

  23. Quantitative probing of glycosylated queuosine modifications in tRNA. Methods Enzymol. 2021; 658:73-82. View in: PubMed

  24. Circadian regulation of apolipoprotein gene expression affects testosterone production in mouse testis. Theriogenology. 2021 Oct 15; 174:9-19. View in: PubMed

  25. ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing. Nat Cell Biol. 2021 07; 23(7):684-691. View in: PubMed

  26. Discovery of 2,4-pyrimidinediamine derivatives as potent dual inhibitors of ALK and HDAC. Eur J Med Chem. 2021 Nov 15; 224:113672. View in: PubMed

  27. Pseudouridine RNA modification detection and quantification by RT-PCR. Methods. 2022 07; 203:1-4. View in: PubMed

  28. Tissue-specific reprogramming of host tRNA transcriptome by the microbiome. Genome Res. 2021 06; 31(6):947-957. View in: PubMed

  29. CMT2N-causing aminoacylation domain mutants enable Nrp1 interaction with AlaRS. Proc Natl Acad Sci U S A. 2021 03 30; 118(13). View in: PubMed

  30. Quantification of Queuosine Modification Levels in tRNA from Human Cells Using APB Gel and Northern Blot. Bio Protoc. 2019 Mar 20; 9(6):e3191. View in: PubMed

  31. [Clinical analysis of 21 cases of cholesteatoma recidivism after canal-wall-up mastoidectomy with tympanoplasty]. Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi. 2021 01 05; 35(1):66-69. View in: PubMed

  32. Management of magnetic foreign body ingestion in children. Medicine (Baltimore). 2021 Jan 15; 100(2):e24055. View in: PubMed

  33. A high-throughput screening method for evolving a demethylase enzyme with improved and new functionalities. Nucleic Acids Res. 2021 03 18; 49(5):e30. View in: PubMed

  34. Inhibition of DNA-PK by gefitinib causes synergism between gefitinib and cisplatin in NSCLC. Int J Oncol. 2020 10; 57(4):939-955. View in: PubMed

  35. Natural polyphenols enhanced the Cu(II)/peroxymonosulfate (PMS) oxidation: The contribution of Cu(III) and HO?. Water Res. 2020 Nov 01; 186:116326. View in: PubMed

  36. A novel peroxymonosulfate (PMS)-enhanced iron coagulation process for simultaneous removal of trace organic pollutants in water. Water Res. 2020 Oct 15; 185:116136. View in: PubMed

  37. Cross-editing by a tRNA synthetase allows vertebrates to abundantly express mischargeable tRNA without causing mistranslation. Nucleic Acids Res. 2020 07 09; 48(12):6445-6457. View in: PubMed

  38. Detection and quantification of glycosylated queuosine modified tRNAs by acid denaturing and APB gels. RNA. 2020 09; 26(9):1291-1298. View in: PubMed

  39. 5-Methylcytosine RNA Modifications Promote Retrovirus Replication in an ALYREF Reader Protein-Dependent Manner. J Virol. 2020 06 16; 94(13). View in: PubMed

  40. tRNA Queuosine Modification Enzyme Modulates the Growth and Microbiome Recruitment to Breast Tumors. Cancers (Basel). 2020 Mar 09; 12(3). View in: PubMed

  41. HIV protease cleaves the antiviral m6A reader protein YTHDF3 in the viral particle. PLoS Pathog. 2020 02; 16(2):e1008305. View in: PubMed

  42. A dual function PUS enzyme. Nat Chem Biol. 2020 02; 16(2):107-108. View in: PubMed

  43. Oxidation of tetrabromobisphenol A (TBBPA) by peroxymonosulfate: The role of in-situ formed HOBr. Water Res. 2020 Feb 01; 169:115202. View in: PubMed

  44. 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 09 24; 116(39):19440-19448. View in: PubMed

  45. Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG. Mol Cell. 2019 10 03; 76(1):70-81.e9. View in: PubMed

  46. Long noncoding RNA LINC00511 promotes cell growth and invasion in triple-negative breast cancer by interacting with Snail. Cancer Manag Res. 2019; 11:5691-5699. View in: PubMed

  47. Discovery of novel 9H-purin derivatives as dual inhibitors of HDAC1 and CDK2. Bioorg Med Chem Lett. 2019 08 15; 29(16):2136-2140. View in: PubMed

  48. Sensitive and quantitative probing of pseudouridine modification in mRNA and long noncoding RNA. RNA. 2019 09; 25(9):1218-1225. View in: PubMed

  49. Ceftriaxone-induced immune hemolytic anemia in a case with large vestibular aqueduct syndrome after cochlear implant. Chin Med J (Engl). 2019 Jan 05; 132(1):100-102. View in: PubMed

  50. Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome. Cell Res. 2019 02; 29(2):167-170. View in: PubMed

  51. Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis. Nat Commun. 2018 12 17; 9(1):5353. View in: PubMed

  52. N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat Chem Biol. 2019 01; 15(1):88-94. View in: PubMed

  53. RNA modification landscape of the human mitochondrial tRNALys regulates protein synthesis. Nat Commun. 2018 09 27; 9(1):3966. View in: PubMed

  54. Methods for Identification of Protein-RNA Interaction. Adv Exp Med Biol. 2018; 1094:117-126. View in: PubMed

  55. Queuosine modification protects cognate tRNAs against ribonuclease cleavage. RNA. 2018 10; 24(10):1305-1313. View in: PubMed

  56. Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing. RNA Biol. 2018; 15(7):892-900. View in: PubMed

  57. An additional class of m6A readers. Nat Cell Biol. 2018 03; 20(3):230-232. View in: PubMed

  58. Modifications and functional genomics of human transfer RNA. Cell Res. 2018 Apr; 28(4):395-404. View in: PubMed

  59. Multifaceted behavior of Meckel's diverticulum in children. J Pediatr Surg. 2018 Apr; 53(4):676-681. View in: PubMed

  60. Dynamic RNA Modifications in Gene Expression Regulation. Cell. 2017 Jun 15; 169(7):1187-1200. View in: PubMed

  61. Determination of tRNA aminoacylation levels by high-throughput sequencing. Nucleic Acids Res. 2017 Aug 21; 45(14):e133. View in: PubMed

  62. Identification of N6-methyladenosine reader proteins. Methods. 2017 08 15; 126:105-111. View in: PubMed

  63. 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. View in: PubMed

  64. N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein. Nucleic Acids Res. 2017 Jun 02; 45(10):6051-6063. View in: PubMed

  65. Hili Inhibits HIV Replication in Activated T Cells. J Virol. 2017 06 01; 91(11). View in: PubMed

  66. RNA modifications and structures cooperate to guide RNA-protein interactions. Nat Rev Mol Cell Biol. 2017 03; 18(3):202-210. View in: PubMed

  67. Function and origin of mistranslation in distinct cellular contexts. Crit Rev Biochem Mol Biol. 2017 Apr; 52(2):205-219. View in: PubMed

  68. tRNA Misacylation with Methionine in the Mouse Gut Microbiome in Situ. Microb Ecol. 2017 07; 74(1):10-14. View in: PubMed

  69. ALKBH1-Mediated tRNA Demethylation Regulates Translation. Cell. 2016 Oct 20; 167(3):816-828.e16. View in: PubMed

  70. 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. View in: PubMed

  71. Determining the fidelity of tRNA aminoacylation via microarrays. Methods. 2017 01 15; 113:27-33. View in: PubMed

  72. 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. View in: PubMed

  73. tRNA base methylation identification and quantification via high-throughput sequencing. RNA. 2016 11; 22(11):1771-1784. View in: PubMed

  74. Codon optimality controls differential mRNA translation during amino acid starvation. RNA. 2016 11; 22(11):1719-1727. View in: PubMed

  75. Structures of the m(6)A Methyltransferase Complex: Two Subunits with Distinct but Coordinated Roles. Mol Cell. 2016 07 21; 63(2):183-185. View in: PubMed

  76. Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis. Adv Nutr. 2016 07; 7(4):773S-9S. View in: PubMed

  77. Interaction of tRNA with MEK2 in pancreatic cancer cells. Sci Rep. 2016 06 15; 6:28260. View in: PubMed

  78. RNA modifications: what have we learned and where are we headed? Nat Rev Genet. 2016 06; 17(6):365-72. View in: PubMed

  79. The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature. 2016 Feb 25; 530(7591):441-6. View in: PubMed

  80. N6-methyladenosine?encoded epitranscriptomics. Nat Struct Mol Biol. 2016 Feb; 23(2):98-102. View in: PubMed

  81. Correction: Methionine Mistranslation Bypasses the Restraint of the Genetic Code to Generate Mutant Proteins with Distinct Activities. PLoS Genet. 2016 01; 12(1):e1005832. View in: PubMed

  82. A dual fluorescent reporter for the investigation of methionine mistranslation in live cells. RNA. 2016 Mar; 22(3):467-76. View in: PubMed

  83. Methionine Mistranslation Bypasses the Restraint of the Genetic Code to Generate Mutant Proteins with Distinct Activities. PLoS Genet. 2015 Dec; 11(12):e1005745. View in: PubMed

  84. Correction: Cytohesins/ARNO: The Function in Colorectal Cancer Cells. PLoS One. 2015; 10(12):e0146204. View in: PubMed

  85. Temperature dependent mistranslation in a hyperthermophile adapts proteins to lower temperatures. Nucleic Acids Res. 2016 Jan 08; 44(1):294-303. View in: PubMed

  86. Probing N6-methyladenosine (m6A) RNA Modification in Total RNA with SCARLET. Methods Mol Biol. 2016; 1358:285-92. View in: PubMed

  87. Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress. Cell. 2015 Sep 10; 162(6):1286-98. View in: PubMed

  88. 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. View in: PubMed

  89. Probing RNA Modification Status at Single-Nucleotide Resolution in Total RNA. Methods Enzymol. 2015; 560:149-59. View in: PubMed

  90. Efficient and quantitative high-throughput tRNA sequencing. Nat Methods. 2015 Sep; 12(9):835-837. View in: PubMed

  91. My adventure in tRNA biology, so far. RNA. 2015 Apr; 21(4):707-8. View in: PubMed

  92. N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature. 2015 Feb 26; 518(7540):560-4. View in: PubMed

  93. The Relationship Between EABR and Auditory Performance and Speech Intelligibility Outcomes in Pediatric Cochlear Implant Recipients. Am J Audiol. 2015 Jun; 24(2):226-34. View in: PubMed

  94. 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. View in: PubMed

  95. A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus. PLoS Biol. 2014 Dec; 12(12):e1002015. View in: PubMed

  96. RNA epigenetics. Transl Res. 2015 Jan; 165(1):28-35. View in: PubMed

  97. Angiogenin-cleaved tRNA halves interact with cytochrome c, protecting cells from apoptosis during osmotic stress. Mol Cell Biol. 2014 Jul; 34(13):2450-63. View in: PubMed

  98. Diversity of human tRNA genes from the 1000-genomes project. RNA Biol. 2013 Dec; 10(12):1853-67. View in: PubMed

  99. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014 Jan 02; 505(7481):117-20. View in: PubMed

  100. Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. RNA. 2013 Dec; 19(12):1848-56. View in: PubMed

  101. [Effects of neoadjuvant chemotherapy on the prognostic mortality risk of invasive transitional bladder cancer: a meta-analysis]. Zhonghua Yi Xue Za Zhi. 2013 Jun 11; 93(22):1705-10. View in: PubMed

  102. Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress. PLoS Genet. 2013 Aug; 9(8):e1003767. View in: PubMed

  103. Adaptive translation as a mechanism of stress response and adaptation. Annu Rev Genet. 2013; 47:121-37. View in: PubMed

  104. Mitochondrial genome of Protobothrops dabieshanensis (Squamata: Viperidae: Crotalinae). Mitochondrial DNA. 2014 Oct; 25(5):337-8. View in: PubMed

  105. Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface. Cell Rep. 2013 May 30; 3(5):1703-13. View in: PubMed

  106. [Electrophysiological characteristics of EABR and its value assessment of cochlear implant]. Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi. 2013 Jan; 27(1):8-12. View in: PubMed

  107. A self-defeating anabolic program leads to ?-cell apoptosis in endoplasmic reticulum stress-induced diabetes via regulation of amino acid flux. J Biol Chem. 2013 Jun 14; 288(24):17202-13. View in: PubMed

  108. Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J Nanobiotechnology. 2013 Apr 03; 11:8. View in: PubMed

  109. 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. View in: PubMed

  110. Function and mode of action of cytohesins in the epidermal growth factor pathway in colorectal cancer cells. Oncol Lett. 2013 Feb; 5(2):521-526. View in: PubMed

  111. N6-methyl-adenosine modification in messenger and long non-coding RNA. Trends Biochem Sci. 2013 Apr; 38(4):204-9. View in: PubMed

  112. 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. View in: PubMed

  113. Vaccinia and influenza A viruses select rather than adjust tRNAs to optimize translation. Nucleic Acids Res. 2013 Feb 01; 41(3):1914-21. View in: PubMed

  114. 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. View in: PubMed

  115. Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress. J Biol Chem. 2012 Dec 14; 287(51):42708-25. View in: PubMed

  116. Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11. Nature. 2012 Nov 01; 491(7422):125-8. View in: PubMed

  117. Anti-tumor effects of an engineered "killer" transfer RNA. Biochem Biophys Res Commun. 2012 Oct 12; 427(1):148-53. View in: PubMed

  118. Misacylation of tRNA with methionine in Saccharomyces cerevisiae. Nucleic Acids Res. 2012 Nov 01; 40(20):10494-506. View in: PubMed

  119. Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I. Science. 2012 Jun 29; 336(6089):1719-23. View in: PubMed

  120. Meta-analysis of randomized controlled trials on laparoscopic gastrectomy vs. open gastrectomy for distal gastric cancer. Hepatogastroenterology. 2012 Sep; 59(118):1699-705. View in: PubMed

  121. A role for tRNA modifications in genome structure and codon usage. Cell. 2012 Mar 30; 149(1):202-13. View in: PubMed

  122. 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. View in: PubMed

  123. Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons. RNA. 2012 Mar; 18(3):355-67. View in: PubMed

  124. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol. 2011 Oct 16; 7(12):885-7. View in: PubMed

  125. tRNA: Vast reservoir of RNA molecules with unexpected regulatory function. Proc Natl Acad Sci U S A. 2011 Oct 04; 108(40):16489-90. View in: PubMed

  126. Cellular dynamics of RNA modification. Acc Chem Res. 2011 Dec 20; 44(12):1380-8. View in: PubMed

  127. 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. View in: PubMed

  128. 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. View in: PubMed

  129. Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature. 2010 Dec 09; 468(7325):784-9. View in: PubMed

  130. Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy. J Am Chem Soc. 2010 Nov 24; 132(46):16352-3. View in: PubMed

  131. RNA folding during transcription: protocols and studies. Methods Enzymol. 2009; 468:167-93. View in: PubMed

  132. Selective control of amino acid metabolism by the GCN2 eIF2 kinase pathway in Saccharomyces cerevisiae. BMC Biochem. 2010 Aug 04; 11:29. View in: PubMed

  133. 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. View in: PubMed

  134. Genome-wide analysis of aminoacylation (charging) levels of tRNA using microarrays. J Vis Exp. 2010 Jun 18; (40). View in: PubMed

  135. Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs. RNA. 2010 Jul; 16(7):1317-27. View in: PubMed

  136. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell. 2010 Apr 16; 141(2):344-54. View in: PubMed

  137. 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. View in: PubMed

  138. 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. View in: PubMed

  139. Functional analysis of human tRNA isodecoders. J Mol Biol. 2010 Feb 26; 396(3):821-31. View in: PubMed

  140. Profiling non-lysyl tRNAs in HIV-1. RNA. 2010 Feb; 16(2):267-73. View in: PubMed

  141. Innate immune and chemically triggered oxidative stress modifies translational fidelity. Nature. 2009 Nov 26; 462(7272):522-6. View in: PubMed

  142. tRNA over-expression in breast cancer and functional consequences. Nucleic Acids Res. 2009 Nov; 37(21):7268-80. View in: PubMed

  143. Genome-wide analysis of tRNA charging and activation of the eIF2 kinase Gcn2p. J Biol Chem. 2009 Sep 11; 284(37):25254-67. View in: PubMed

  144. 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. View in: PubMed

  145. Efficient chemical synthesis of AppDNA by adenylation of immobilized DNA-5'-monophosphate. Org Lett. 2009 Mar 05; 11(5):1067-70. View in: PubMed

  146. 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. View in: PubMed

  147. Probing RNA structure by lead cleavage. Curr Protoc Nucleic Acid Chem. 2001 May; Chapter 6:Unit 6.3. View in: PubMed

  148. A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics. J Mol Biol. 2008 May 09; 378(4):943-53. View in: PubMed

  149. 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. View in: PubMed

  150. Folding of a universal ribozyme: the ribonuclease P RNA. Q Rev Biophys. 2007 May; 40(2):113-61. View in: PubMed

  151. Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine. Nucleic Acids Res. 2007; 35(18):6322-9. View in: PubMed

  152. 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. View in: PubMed

  153. Tissue-specific differences in human transfer RNA expression. PLoS Genet. 2006 Dec; 2(12):e221. View in: PubMed

  154. Diversity of tRNA genes in eukaryotes. Nucleic Acids Res. 2006; 34(21):6137-46. View in: PubMed

  155. A systematic, ligation-based approach to study RNA modifications. RNA. 2006 Nov; 12(11):2025-33. View in: PubMed

  156. RNA folding during transcription. Annu Rev Biophys Biomol Struct. 2006; 35:161-75. View in: PubMed

  157. Structure of ribonuclease P--a universal ribozyme. Curr Opin Struct Biol. 2006 Jun; 16(3):327-35. View in: PubMed

  158. Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium. RNA. 2006 Apr; 12(4):598-606. View in: PubMed

  159. An aggregation-specific enzyme-linked immunosorbent assay: detection of conformational differences between recombinant PrP protein dimers and PrP(Sc) aggregates. J Virol. 2005 Oct; 79(19):12355-64. View in: PubMed

  160. 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. View in: PubMed

  161. Crystal structure of the RNA component of bacterial ribonuclease P. Nature. 2005 Sep 22; 437(7058):584-7. View in: PubMed

  162. Real-time RNA profiling within a single bacterium. Proc Natl Acad Sci U S A. 2005 Jun 28; 102(26):9160-4. View in: PubMed

  163. Mechanistic insights on the folding of a large ribozyme during transcription. Biochemistry. 2005 May 24; 44(20):7535-42. View in: PubMed

  164. Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO Rep. 2005 Feb; 6(2):151-7. View in: PubMed

  165. Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization. RNA. 2005 Feb; 11(2):234-9. View in: PubMed

  166. Biochemical fingerprints of prion infection: accumulations of aberrant full-length and N-terminally truncated PrP species are common features in mouse prion disease. J Virol. 2005 Jan; 79(2):934-43. View in: PubMed

  167. Basis for structural diversity in homologous RNAs. Science. 2004 Oct 01; 306(5693):104-7. View in: PubMed

  168. Reduced contact order and RNA folding rates. J Mol Biol. 2004 Oct 01; 342(5):1359-65. View in: PubMed

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