Pan:Methods: Difference between revisions

From OpenWetWare
Jump to navigationJump to search

Pan:Methods (view source)

Revision as of 12:34, 26 December 2018

639 bytes added ,  26 December 2018
no edit summary
No edit summary
No edit summary
Line 1: Line 1:


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


''(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).
''(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).  


''(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 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).


''(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).
''(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).


''(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).
''(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:'''
'''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)'' 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).  
''(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).
''(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 e1002015, p.1-13 (2014).
''(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).
''(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 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).


''(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 biology:'''


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


'''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).
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).
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).




Taopan
198

edits

Retrieved from "https://openwetware.org/wiki/Special:MobileDiff/1056452"

Navigation menu