Pseudouridine in mRNA: Incorporation, Detection, and Recoding

Methods in Enzymology

Volumn 560, Issue , 2015, Pages 187-217

  Wu, Guowei ^a   Huang, Chao ^b   Yu, Yi Tao ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b BRISTOL MYERS SQUIBB COMPANY   (United States)

^c UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

Author keywords

Box H ACA RNP; Nonsense suppression; Premature termination codon; Pseudouridine; Pseudouridylation; RNA modification

Indexed keywords

ADENOSINE TRIPHOSPHATE; DNA; MESSENGER RNA; NUCLEASE; NUCLEOTIDE; PHOSPHORUS 32; PSEUDOURIDINE; RIBONUCLEASE H; RIBONUCLEOPROTEIN; RIBOSOME RNA; SMALL NUCLEAR RNA; STOP CODON; TRANSFER RNA;

ARTICLE; CHIMERA; CODON; DEPHOSPHORYLATION; ENZYME ACTIVITY; GENE EXPRESSION; ISOTOPE LABELING; MUTAGENESIS; NONHUMAN; NUCLEOTIDE METABOLISM; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA ISOLATION; SACCHAROMYCES CEREVISIAE; WESTERN BLOTTING; YEAST; ANIMAL; CHEMISTRY; CONFORMATION; GENETICS; HUMAN; ISOLATION AND PURIFICATION; METABOLISM; STOP CODON; XENOPUS LAEVIS;

EUKARYOTA; XENOPUS LAEVIS;

ANIMALS; CODON, TERMINATOR; HUMANS; NUCLEIC ACID CONFORMATION; PSEUDOURIDINE; RIBONUCLEOPROTEINS; RNA, MESSENGER; RNA, RIBOSOMAL; RNA, SMALL NUCLEAR; RNA, TRANSFER; XENOPUS LAEVIS;

EID: 84938989051     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/bs.mie.2015.03.009     Document Type: Chapter

References (24)

1. H. Adachi, and Y.T. Yu Purification of radiolabeled RNA products using denaturing gel electrophoresis Current Protocols in Molecular Biology 105 2014 10.1002/0471142727.mb0420s105 4.20.1-4.20.13
2. Y. Bilbille, F.A. Vendeix, R. Guenther, A. Malkiewicz, X. Ariza, J. Vilarrasa, and et al. The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs Nucleic Acids Research 37 10 2009 3342 3353 10.1093/nar/gkp187
3. T.M. Carlile, M.F. Rojas-Duran, B. Zinshteyn, H. Shin, K.M. Bartoli, and W.V. Gilbert Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells Nature 515 7525 2014 143 146 10.1038/nature13802
4. I. Chernyakov, J.M. Whipple, L. Kotelawala, E.J. Grayhack, and E.M. Phizicky Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5′-3′ exonucleases Rat1 and Xrn1 Genes & Development 22 10 2008 1369 1380 10.1101/gad.1654308
5. D.R. Davis Stabilization of RNA stacking by pseudouridine Nucleic Acids Research 23 24 1995 5020 5026
6. F.F. Davis, and F.W. Allen Ribonucleic acids from yeast which contain a fifth nucleotide The Journal of Biological Chemistry 227 2 1957 907 915
7. P.C. Durant, and D.R. Davis Stabilization of the anticodon stem-loop of tRNALys,3 by an A + - C base-pair and by pseudouridine Journal of Molecular Biology 285 1 1999 115 131 10.1006/jmbi.1998.2297
8. I.S. Fernandez, C.L. Ng, A.C. Kelley, G. Wu, Y.T. Yu, and V. Ramakrishnan Unusual base pairing during the decoding of a stop codon by the ribosome Nature 500 7460 2013 107 110 10.1038/nature12302
9. J. Ge, and Y.T. Yu RNA pseudouridylation: New insights into an old modification Trends in Biochemical Sciences 38 4 2013 210 218 10.1016/j.tibs.2013.01.002
10. C. Huang, J. Karijolich, and Y.T. Yu Post-transcriptional modification of RNAs by artificial box H/ACA and box C/D RNPs Methods in Molecular Biology 718 2011 227 244 10.1007/978-1-61779-018-8-14
11. C. Huang, G. Wu, and Y.T. Yu Inducing nonsense suppression by targeted pseudouridylation Nature Protocols 7 4 2012 789 800 10.1038/nprot.2012.029
12. C. Huang, and Y.T. Yu Synthesis and labeling of RNA in vitro Current Protocols in Molecular Biology 4 2013 Unit4.15 10.1002/0471142727.mb0415s102
13. J. Karijolich, and Y.T. Yu Insight into the protein components of the box H/ACA RNP Current Proteomics 5 2 2008 129 137 10.2174/157016408784911936
14. J. Karijolich, and Y.T. Yu Converting nonsense codons into sense codons by targeted pseudouridylation Nature 474 7351 2011 395 398 10.1038/nature10165
15. T.H. King, B. Liu, R.R. McCully, and M.J. Fournier Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center Molecular Cell 11 2 2003 425 435
16. F. Lecointe, O. Namy, I. Hatin, G. Simos, J.P. Rousset, and H. Grosjean Lack of pseudouridine 38/39 in the anticodon arm of yeast cytoplasmic tRNA decreases in vivo recoding efficiency The Journal of Biological Chemistry 277 34 2002 30445 30453 10.1074/jbc.M203456200
17. C.H. Lee, and I. Tinoco Jr. Conformation studies of 13 trinucleoside diphosphates by 360 MHz PMR spectroscopy. A bulged base conformation. I. Base protons and H1′ protons Biophysical Chemistry 11 2 1980 283 294 http://dx.doi.org/0301-4622(80)80031-7 [pii]
18. X.H. Liang, Q. Liu, and M.J. Fournier rRNA modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activity Molecular Cell 28 6 2007 965 977 10.1016/j.molcel.2007.10.012
19. A.F. Lovejoy, D.P. Riordan, and P.O. Brown Transcriptome-wide mapping of pseudouridines: Pseudouridine synthases modify specific mRNAs in S. cerevisiae PLoS One 9 10 2014 e110799 10.1371/journal.pone.0110799
20. X. Ma, C. Yang, A. Alexandrov, E.J. Grayhack, I. Behm-Ansmant, and Y.T. Yu Pseudouridylation of yeast U2 snRNA is catalyzed by either an RNA-guided or RNA-independent mechanism The EMBO Journal 24 13 2005 2403 2413
21. S. Schwartz, D.A. Bernstein, M.R. Mumbach, M. Jovanovic, R.H. Herbst, B.X. Leon-Ricardo, and et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA Cell 159 1 2014 148 162 10.1016/j.cell.2014.08.028
22. G. Wu, A.T. Yu, A. Kantartzis, and Y.T. Yu Functions and mechanisms of spliceosomal small nuclear RNA pseudouridylation Wiley Interdisciplinary Reviews. RNA 2 4 2011 571 581 10.1002/wrna.77
23. Y.T. Yu Construction of 4-thiouridine site-specifically substituted RNAs for cross-linking studies Methods 18 1 1999 13 21 10.1006/meth.1999.0752
24. Y.T. Yu, M.D. Shu, and J.A. Steitz Modifications of U2 snRNA are required for snRNP assembly and pre-mRNA splicing The EMBO Journal 17 19 1998 5783 5795