Pan:Methods

DM-tRNA-seq (demethylase tRNA-seq):

(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:

(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 modifications 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 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:

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).

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

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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