Pan:Methods

tRNA-seq and small RNA-seq

(Single-read analysis of coordination) Hernandez-Alias, X., C.D. Katanski, W. Zhang, M. Assari, C.P. Watkins, M.H. Schaefer, L. Serrano, Tao Pan*: Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation, Nucl. Acids Res. 51, e17 (2023).

(Multiplex Small RNA sequencing, MSR-seq) Watkins, C.P., W. Zhang, A.C. Wylder, C.D. Katanski*, Tao Pan*: A multiplex platform for small RNA sequencing elucidates multifaceted tRNA stress response and translational regulation, Nature Communications 13, 2491 (2022).

(Demethylase screening) Wang, Y.U., C.D. Katanski, C. Watkins, J.N. Pan, Q. Dai, Z-X. Jiang, Tao Pan*: A High-throughput Screening Method for Evolving a Demethylase Enzyme with Improved and New Functionalities, Nucl. Acids Res. 49, e30 (2021).

(Microbiome) Schwartz, M.H., H.P. Wang, J.N. Pan, W.C. Clark, S. Cui, M.J. Eckwahl, D.W. Pan, M. Parisien, S.M. Owens, B.L. Cheng, K. Martinez, J.B. Xu, E.B. Chang, Tao Pan*, A.M. Eren*: Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis, Nature Communications 9:5353, p.1-13 (2018).

(tRNA charging) Evans, M.E., W.C. Clark, G-Q. Zheng & Tao Pan*: Determination of tRNA aminoacylation levels by high throughput sequencing, Nucl. Acids Res. 45, e133, p.1-8 (2017).

(m22G demethylase) Dai, Q., G-Q. Zheng, M.H. Schwartz, W.C. Clark & Tao Pan*: Selective enzymatic demethylation of N2,N2-dimethylguanosine in RNA and its application in high-throughput tRNA sequencing, Angewandte Chemie (Int) 56, 5017-5020 (2017).

(tRNA modification) 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).

(DM-tRNA-seq) 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).

RNA modification

(Nanopore simultaneous m6A and pseudouridine) Huang, S-H., A.C. Wylder, Tao Pan*: Simultaneous mRNA m6A and Pseudouridine Nanopore Profiling Reveals Coordination in Translation, Nature Biotech. in press (2024).

(Queuosine and 2-thio) Katanski, C.D., C.P. Watkins, W. Zhang, M. Reyer, S. Miller, Tao Pan*: Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing, Nucl. Acids Res. 50, e99 (2022).

(Nanopore pseudouridine) Huang, S. W. Zhang, C.D. Katanski, D. Dersh, Q. Dai, K. Lolans, J. Yewdell, A.M. Eren, Tao Pan*: Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling, Genome Biology 22, 330 (2021).

(Glycosylated queuosine) Zhang, W., R-Y. Xu, Z. Matuszek, Z. Cai, Tao Pan*: Detection and quantification of glycosylated queuosine modified tRNAs by acid denaturing and APB gels, RNA 26, 1291-1298 (2020).

(CLAP) Zhang, W., M.J. Eckwahl, K.I. Zhou, Tao Pan*: Sensitive and quantitative probing of pseudouridine modification in mRNA and long non-coding RNA, RNA 25, 1218-1225 (2019).

(m6A reader protein) Zhou, K.I., N. Liu & Tao Pan*: Identification of N6-methyladenosine reader proteins, Methods 126, 105-111 (2017).

(m6A reader protein) 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).

(SCARLET) Liu, N. & Tao Pan*: Probing RNA modification status at single-nucleotide resolution in total RNA, Methods in Enzymology 560, 149-59 (2015).

(tRNA Q-modification) Zaborske, J.M., V. L. DuMont, E. W. J. Wallace, Tao Pan, C. F. Aquadro & D. A. Drummond: A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus, PLoS Biology 13, e1002015, p.1-13 (2014).

(SCARLET) 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).

(RNA modification by ligation) Dai, Q., R. Fong, M. Saikia, D. Stephenson, Y.-T. Yu, Tao Pan* & J.A. Piccirill*: Identification of Recognition Residues for Ligation-Based Detection and Quantitation of Pseudouridine and N6-Methyladeonsine, Nucl. Acids Res. 35, 6322-6329 (2007).

(RNA modification by ligation) 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).

tRNA biology

(tRNA m1A modification, qPCR) Zhang, W., H. Chen, M. Sobczyk, D. Krochmal, C.D. Katanski, M. Assari, A. Chen, Y. Hou, Q. Dai, Tao Pan*: Quantification of tRNA m1A modification by templated-ligation qPCR, RNA, in press (2024).

(tRNA microarray, misacylation) Schwartz*, M.H., Tao Pan*: Determining the fidelity of tRNA aminoacylation via microarrays, Methods 113, 27-33 (2017).

(tRNA microarray, microbiome) Schwartz*, M.H. & Tao Pan*: tRNA misacylation with methionine in the mouse gut microbiome in situ, Microbial Ecology 74, 10-14 (2017).

(Mistranslation reporter cells) 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).

(tRNA genes in human population) Parisien, M., X. Wang, Tao Pan*: Diversity of human tRNA genes from the 1,000-genomes project, RNA Biology 10, 1853-1867 (2013).

(New tRNA binding proteins) 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).

(tRNA microarray, charging) 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).

(tRNA isodecoder analysis) Geslain, R. & Tao Pan*: Functional analysis of human tRNA isodecoders, J. Mol. Biol. 396, 821-831 (2010).

(tRNA misacylation) 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).

(tRNA microarray, charging) Dittmar, K.A., M. Sorensen, J. Elf, M. Ehrenberg & Tao Pan*: Selective charging of tRNA isoacceptors induced by amino acid starvation. EMBO Reports 6, 151-157 (2005).

Co-transcriptional RNA folding

(Riboswitch) 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).

(Riboswitch) Wong, T.N. & Tao Pan*: RNA Folding during Transcription: Protocols and Studies. Methods in Enzymology 468, 167-193 (2009).

(Ribozyme) 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).

Tertiary RNA folding

(Metal ion in rate-liming step) 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).

(SAXS) Fang, X-W., K.L. Littrell, X-J. Yang, S.J. Henderson, S. Seifert, P. Thiyagarajan, Tao Pan* & T.R. Sosnick*: Mg2+-dependent compaction and folding of the yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by Small-angle X-ray scattering. Biochemistry 39, 11107-11113 (2000).

(Quantitative denaturation) Shelton, V., T.R. Sosnick* & Tao Pan*: The applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding. Biochemistry 38, 16831-16839 (1999).

(Kinetic framework) Fang, X-W., Tao Pan* & T.R. Sosnick*: Mg2+-dependent folding of a large ribozyme without kinetic traps. Nature Str. Mol. Biol. 6, 1091-1095 (1999).

(Spectroscopy) Tao Pan* & T.R. Sosnick*: Intermediates and kinetic traps in the folding of a large ribozyme revealed by CD spectroscopy and catalytic activity. Nature Str. Mol. Biol. 4, 931-938 (1997).

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