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Yi-Tao Yu, Ph.D.


Showing all 75 journal articles & 2 books available

Journal Articles

Adachi H, DeZoysa MD, Yu YT. "Detection and Quantification of Pseudouridine in RNA." Methods in molecular biology.. 2019 1870:219-235.

Adachi H, De Zoysa MD, Yu YT. "Post-transcriptional pseudouridylation in mRNA as well as in some major types of noncoding RNAs." Biochimica et biophysica acta. Gene regulatory mechanisms.. 2018 Nov 8; Epub 2018 Nov 08.

De Zoysa MD, Wu G, Katz R, Yu YT. "Guide-substrate base-pairing requirement for box H/ACA RNA-guided RNA pseudouridylation." RNA.. 2018 Aug; 24(8):1106-1117. Epub 2018 Jun 05.

Zhao Y, Dunker W, Yu YT, Karijolich J. "The Role of Noncoding RNA Pseudouridylation in Nuclear Gene Expression Events." Frontiers in bioengineering and biotechnology.. 2018 6:8. Epub 2018 Feb 08.

Ge J, Karijolich J, Zhai Y, Zheng J, Yu YT. "5-Fluorouracil Treatment Alters the Efficiency of Translational Recoding." Genes.. 2017 Oct 31; 8(11)Epub 2017 Oct 31.

Poole AR, Vicino I, Adachi H, Yu YT, Hebert MD. "Regulatory RNPs: a novel class of ribonucleoproteins that potentially contribute to ribosome heterogeneity." Biology open.. 2017 Sep 15; 6(9):1342-1354. Epub 2017 Sep 15.

De Zoysa MD, Yu YT. "Posttranscriptional RNA Pseudouridylation." The Enzymes.. 2017 41:151-167. Epub 2017 Mar 11.

Xu C, Ishikawa H, Izumikawa K, Li L, He H, Nobe Y, Yamauchi Y, Shahjee HM, Wu XH, Yu YT, Isobe T, Takahashi N, Min J. "Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly." Genes & development.. 2016 Nov 1; 30(21):2376-2390. Epub 2016 Nov 10.

Wu G, Radwan MK, Xiao M, Adachi H, Fan J, Yu YT. "The TOR signaling pathway regulates starvation-induced pseudouridylation of yeast U2 snRNA." RNA.. 2016 Aug; 22(8):1146-52. Epub 2016 Jun 07.

Huang C, Karijolich J, Yu YT. "Detection and quantification of RNA 2'-O-methylation and pseudouridylation." Methods : a companion to Methods in enzymology.. 2016 Jul 1; 103:68-76. Epub 2016 Feb 04.

Wu G, Adachi H, Ge J, Stephenson D, Query CC, Yu YT. "Pseudouridines in U2 snRNA stimulate the ATPase activity of Prp5 during spliceosome assembly." The EMBO journal.. 2016 Mar 15; 35(6):654-67. Epub 2016 Feb 12.

Huang C, Wu G, Yu YT. "Purification and Functional Reconstitution of Box H/ACA Ribonucleoprotein Particles." Methods in molecular biology.. 2016 1421:97-109.

Karijolich J, Yi C, Yu YT. "Transcriptome-wide dynamics of RNA pseudouridylation." Nature reviews. Molecular cell biology.. 2015 Oct; 16(10):581-5. Epub 2015 Aug 19.

Karijolich J, Yu YT. "The new era of RNA modification." RNA.. 2015 Apr; 21(4):659-60.

Enwerem II, Wu G, Yu YT, Hebert MD. "Cajal body proteins differentially affect the processing of box C/D scaRNPs." PloS one.. 2015 10(4):e0122348. Epub 2015 Apr 13.

Wu G, Huang C, Yu YT. "Pseudouridine in mRNA: Incorporation, Detection, and Recoding." Methods in enzymology.. 2015 560:187-217. Epub 2015 Apr 27.

Adachi H, Yu YT. "Insight into the mechanisms and functions of spliceosomal snRNA pseudouridylation." World journal of biological chemistry. 2014 Nov 26; 5(4):398-408.

Karijolich J, Yu YT. "Therapeutic suppression of premature termination codons: mechanisms and clinical considerations (review)." International journal of molecular medicine.. 2014 Aug; 34(2):355-62. Epub 2014 Jun 17.

Adachi H, Yu YT. "Purification of radiolabeled RNA products using denaturing gel electrophoresis." Current protocols in molecular biology. 2014 Jan 6; 105:Unit 4.20.. Epub 2014 Jan 06.

Jun Lim S, Scott A, Xiong XP, Vahidpour S, Karijolich J, Guo D, Pei S, Yu YT, Zhou R, Li W. "Requirement for CRIF1 in RNA interference and Dicer-2 stability." RNA biology.. 2014 11(9):1171-9.

Yu YT, Meier UT. "RNA-guided isomerization of uridine to pseudouridine--pseudouridylation." RNA biology.. 2014 11(12):1483-94.

Fernández IS, Ng CL, Kelley AC, Wu G, Yu YT, Ramakrishnan V. "Unusual base pairing during the decoding of a stop codon by the ribosome." Nature.. 2013 Aug 1; 500(7460):107-10. Epub 2013 Jun 30.

Ge J, Yu YT. "RNA pseudouridylation: new insights into an old modification." Trends in biochemical sciences.. 2013 Apr; 38(4):210-8. Epub 2013 Feb 04.

Huang C, Yu YT. "Synthesis and labeling of RNA in vitro." Current protocols in molecular biology. 2013 Apr; Chapter 4:Unit4.15.

Huang, C; Yu, YT. "Synthesis and labeling of RNA in vitro." Wiley Current Protocols in Molecular Biology. 2013; .

Huang C, Wu G, Yu YT. "Inducing nonsense suppression by targeted pseudouridylation." Nature protocols.. 2012 Mar 29; 7(4):789-800. Epub 2012 Mar 29.

Huang, C; Wu, G; Yu, YT. "Inducing nonsense suppression by targeted pseudouridylation." Nature Protocols. 2012; 7: 789-800.

Yu AT, Ge J, Yu YT. "Pseudouridines in spliceosomal snRNAs." Protein & cell. 2011 Sep; 2(9):712-25. Epub 2011 Oct 06.

Karijolich J, Yu YT. "Converting nonsense codons into sense codons by targeted pseudouridylation." Nature.. 2011 Jun 15; 474(7351):395-8. Epub 2011 Jun 15.

Wu G, Xiao M, Yang C, Yu YT. "U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP." The EMBO journal.. 2011 Jan 5; 30(1):79-89. Epub 2010 Dec 03.

Wu G; Yu AT; Kantartzis A; Yu YT. "Functions and Mechanisms of Spliceosomal snRNA pseudouridylation." Wiley Interdisciplinary Reviews (WIREs) RNA. 2011; 2: 571-581.

Yu, AT; Ge, J; Yu, YT. "Pseudouridines in spliceosomal snRNAs." Protein & Cell. 2011; 2: 712-725.

Huang C, Karijolich J, Yu YT. "Post-transcriptional modification of RNAs by artificial Box H/ACA and Box C/D RNPs." Methods in molecular biology.. 2011 718:227-44.

Wu G, Yu AT, Kantartzis A, Yu YT. "Functions and mechanisms of spliceosomal small nuclear RNA pseudouridylation." Wiley interdisciplinary reviews. RNA.. 2011 2(4):571-81. Epub 2011 Feb 18.

Chen C, Zhao X, Kierzek R, Yu YT. "A flexible RNA backbone within the polypyrimidine tract is required for U2AF65 binding and pre-mRNA splicing in vivo." Molecular and cellular biology.. 2010 Sep; 30(17):4108-19. Epub 2010 Jul 06.

Huang C, Yu YT. "Targeted 2'-O methylation at a nucleotide within the pseudoknot of telomerase RNA reduces telomerase activity in vivo." Molecular and cellular biology.. 2010 Sep; 30(18):4368-78. Epub 2010 Jul 20.

Ge J, Liu H, Yu YT. "Regulation of pre-mRNA splicing in Xenopus oocytes by targeted 2'-O-methylation." RNA.. 2010 May; 16(5):1078-85. Epub 2010 Mar 26.

Karijolich J, Yu YT. "Spliceosomal snRNA modifications and their function." RNA biology.. 2010 7(2):192-204. Epub 2010 Mar 14.

Karijolich J, Kantartzis A, Yu YT. "RNA modifications: a mechanism that modulates gene expression." Methods in molecular biology.. 2010 629:1-19.

Karijolich J, Kantartzis A, Yu YT. "Quantitative analysis of RNA modifications." Methods in molecular biology.. 2010 629:21-32.

Xiao M, Yang C, Schattner P, Yu YT. "Functionality and substrate specificity of human box H/ACA guide RNAs." RNA.. 2009 Jan; 15(1):176-86. Epub 2008 Nov 25.

Karijolich, J; Huang, C; Yu, YT. "Spliceosomal snRNA pseudouridylation." In DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution (ed. H. Grosjean). Landes Bioscience. 2009; : 461-474.

Karijolich J, Yu YT. "Insight into the Protein Components of the Box H/ACA RNP." Current proteomics. 2008 Jul 1; 5(2):129-137.

Zhao X, Yu YT. "Targeted pre-mRNA modification for gene silencing and regulation." Nature methods.. 2008 Jan; 5(1):95-100. Epub 2007 Dec 09.

Stephenson, D; Karijolich, J; Yu, YT. "Functional roles of spliceosomal snRNA modifications in pre-mRNA splicing." In RNA and DNA Editing: Molecular Mechanisms and Their Integration into Biological Systems (ed. H. Smith). John Wiley & Sons Press, Hoboken, New Jersey, USA. 2008; : 175-189.

Karijolich, J.; Yu, Y.T.;. "Pre-mRNA splicing" . Wiley Encyclopedia of Chemical Biology. (ed. TP Begley). 2007; : DOI: 10.1002/9780470048672.wecb520. Article Online Posting.

Zhao X, Yu YT. "Incorporation of 5-fluorouracil into U2 snRNA blocks pseudouridylation and pre-mRNA splicing in vivo." Nucleic acids research.. 2007 35(2):550-8. Epub 2006 Dec 14.

Karijolich J, Stephenson D, Yu YT. "Biochemical purification of box H/ACA RNPs involved in pseudouridylation." Methods in enzymology.. 2007 425:241-62.

Dai Q, Fong R, Saikia M, Stephenson D, Yu YT, Pan T, Piccirilli JA. "Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine." Nucleic acids research.. 2007 35(18):6322-9. Epub 2007 Sep 18.

Yu YT. "The most complex pseudouridylase." Structure.. 2006 Feb; 14(2):167-8.

Moon KH, Zhao X, Yu YT. "Pre-mRNA splicing in the nuclei of Xenopus oocytes." Methods in molecular biology.. 2006 322:149-63.

Ma X, Yang C, Alexandrov A, Grayhack EJ, Behm-Ansmant I, Yu YT. "Pseudouridylation of yeast U2 snRNA is catalyzed by either an RNA-guided or RNA-independent mechanism." The EMBO journal.. 2005 Jul 6; 24(13):2403-13. Epub 2005 Jun 16.

Yang C, McPheeters DS, Yu YT. "Psi35 in the branch site recognition region of U2 small nuclear RNA is important for pre-mRNA splicing in Saccharomyces cerevisiae." The Journal of biological chemistry.. 2005 Feb 25; 280(8):6655-62. Epub 2004 Dec 20.

Yu, Y.-T.; Terns, R. M.; Terns, M. P.;. "Mechanisms and functions of RNA-guided RNA modifications". In Fine-tuning of RNA functions by modification and editing, Topics in Current Genetics series, vol. 12 (ed. H. Grosjean). Springer-Verlag Press, New York, USA. 2005; : 223-262. Link

Zhao X, Yu YT. "Detection and quantitation of RNA base modifications." RNA.. 2004 Jun; 10(6):996-1002.

Zhao X, Yu YT. "Pseudouridines in and near the branch site recognition region of U2 snRNA are required for snRNP biogenesis and pre-mRNA splicing in Xenopus oocytes." RNA.. 2004 Apr; 10(4):681-90.

Behm-Ansmant I, Urban A, Ma X, Yu YT, Motorin Y, Branlant C. "The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Psi-synthase also acting on tRNAs." RNA.. 2003 Nov; 9(11):1371-82.

Ma X, Zhao X, Yu YT. "Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism." The EMBO journal.. 2003 Apr 15; 22(8):1889-97.

Zhao X, Li ZH, Terns RM, Terns MP, Yu YT. "An H/ACA guide RNA directs U2 pseudouridylation at two different sites in the branchpoint recognition region in Xenopus oocytes." RNA.. 2002 Dec; 8(12):1515-25.

Yu YT, Shu MD, Narayanan A, Terns RM, Terns MP, Steitz JA. "Internal modification of U2 small nuclear (sn)RNA occurs in nucleoli of Xenopus oocytes." The Journal of cell biology.. 2001 Mar 19; 152(6):1279-88.

Yu YT. "Site-specific 4-thiouridine incorporation into RNA molecules." Methods in enzymology.. 2000 318:71-88.

Yu YT. "Construction of 4-thiouridine site-specifically substituted RNAs for cross-linking studies." Methods : a companion to Methods in enzymology.. 1999 May; 18(1):13-21.

Yu, Y.T.; Scharl, E.C.; Smith, C.M.; Steitz, J.A. ;. "The growing world of small nuclear ribonucleoprotein particles". In The RNA World, 2nd edition (eds. Gesteland, Cech, and Atkins),Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. 1999; : 487-524. Link

Yu YT, Shu MD, Steitz JA. "Modifications of U2 snRNA are required for snRNP assembly and pre-mRNA splicing." The EMBO journal.. 1998 Oct 1; 17(19):5783-95.

Lapham J, Yu YT, Shu MD, Steitz JA, Crothers DM. "The position of site-directed cleavage of RNA using RNase H and 2'-O-methyl oligonucleotides is dependent on the enzyme source." RNA.. 1997 Sep; 3(9):950-1.

Yu YT, Steitz JA. "A new strategy for introducing photoactivatable 4-thiouridine ((4S)U) into specific positions in a long RNA molecule." RNA.. 1997 Jul; 3(7):807-10.

Yu YT, Steitz JA. "Site-specific crosslinking of mammalian U11 and u6atac to the 5' splice site of an AT-AC intron." Proceedings of the National Academy of Sciences of the United States of America.. 1997 Jun 10; 94(12):6030-5.

Yu YT, Shu MD, Steitz JA. "A new method for detecting sites of 2'-O-methylation in RNA molecules." RNA.. 1997 Mar; 3(3):324-31.

Yu YT, Tarn WY, Yario TA, Steitz JA. "More Sm snRNAs from vertebrate cells." Experimental cell research.. 1996 Dec 15; 229(2):276-81.

Maroney PA, Yu YT, Jankowska M, Nilsen TW. "Direct analysis of nematode cis- and trans-spliceosomes: a functional role for U5 snRNA in spliced leader addition trans-splicing and the identification of novel Sm snRNPs." RNA.. 1996 Aug; 2(8):735-45.

Denker JA, Maroney PA, Yu YT, Kanost RA, Nilsen TW. "Multiple requirements for nematode spliced leader RNP function in trans-splicing." RNA.. 1996 Aug; 2(8):746-55.

Yu YT, Maroney PA, Darzynkiwicz E, Nilsen TW. "U6 snRNA function in nuclear pre-mRNA splicing: a phosphorothioate interference analysis of the U6 phosphate backbone." RNA.. 1995 Mar; 1(1):46-54.

Yu YT, Maroney PA, Nilsen TW. "Functional reconstitution of U6 snRNA in nematode cis- and trans-splicing: U6 can serve as both a branch acceptor and a 5' exon." Cell.. 1993 Dec 17; 75(6):1049-59.

Hannon GJ, Maroney PA, Yu YT, Hannon GE, Nilsen TW. "Interaction of U6 snRNA with a sequence required for function of the nematode SL RNA in trans-splicing." Science.. 1992 Dec 11; 258(5089):1775-80.

Yu YT, Nilsen TW. "Sequence requirements for maturation of the 5' terminus of human 18 S rRNA in vitro." The Journal of biological chemistry.. 1992 May 5; 267(13):9264-8.

Books & Chapters

Chapter Title: Spliceosomal snRNA pseudouridylation
Book Title: DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution
Author List: Karijolich, J., Huang, C. and Yu, Y.-T.
Edited By: H. Grosjean
Published By: Landes Bioscience2009 in Austin, Texas

Chapter Title: Functional roles of spliceosomal snRNA modifications in pre-mRNA splicing
Book Title: RNA and DNA Editing: Molecular Mechanisms and Their Integration into Biological
Author List: Stephenson, D., Karijolich, J. and Yu, Y.-T.
Edited By: H. Smith
Published By: John Wiley & Sons Press2008 in Hoboken, New Jersey