Yi-Tao Yu
| Title | Associate Professor |
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| Institution | School of Medicine and Dentistry |
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| Department | Biochemistry and Biophysics |
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| Address | University of Rochester Medical Center
School of Medicine and Dentistry
601 Elmwood Ave, Box 712
Rochester NY 14642
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Our long-range goal is to elucidate the underlying biological principles and functional roles of posttranscriptional RNA modifications. Currently, we are particularly interested in 2'-O-methylation and pseudouridylation in three different types of RNA, including the spliceosomal snRNA involved in pre-mRNA splicing, the telomerase RNA required for telomere length maintenance, and the messenger RNA that encodes a chemical "blueprint" for the production of a protein.
Our recent research has demonstrated that all these three types of RNA can be modified in vivo, either naturally or artificially through the RNA-guided RNA modification mechanisms. Importantly, our experimental data indicate that the posttranscriptional nucleotide modifications contribute significantly to RNA functions. We are currently carrying out three projects, aiming to address some of the fundamental questions regarding RNA modifications.
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Karijolich J, Yu YT. Converting nonsense codons into sense codons by targeted pseudouridylation. Nature. 2011 Jun 16; 474(7351):395-8.
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Huang C, Karijolich J, Yu YT. Post-transcriptional modification of RNAs by artificial Box H/ACA and Box C/D RNPs. Methods Mol Biol. 2011; 718:227-44.
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Wu G, Xiao M, Yang C, Yu YT. U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP. EMBO J. 2011 Jan 5; 30(1):79-89.
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Huang C, Yu YT. Targeted 2'-O methylation at a nucleotide within the pseudoknot of telomerase RNA reduces telomerase activity in vivo. Mol Cell Biol. 2010 Sep; 30(18):4368-78.
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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. Mol Cell Biol. 2010 Sep; 30(17):4108-19.
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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.
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Karijolich J, Yu YT. Spliceosomal snRNA modifications and their function. RNA Biol. 2010 Mar-Apr; 7(2):192-204.
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Karijolich J, Kantartzis A, Yu YT. RNA modifications: a mechanism that modulates gene expression. Methods Mol Biol. 2010; 629:1-19.
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Karijolich J, Kantartzis A, Yu YT. Quantitative analysis of RNA modifications. Methods Mol Biol. 2010; 629:21-32.
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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.
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Zhao X, Yu YT. Targeted pre-mRNA modification for gene silencing and regulation. Nat Methods. 2008 Jan; 5(1):95-100.
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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 Res. 2007; 35(18):6322-9.
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Karijolich J, Stephenson D, Yu YT. Biochemical purification of box H/ACA RNPs involved in pseudouridylation. Methods Enzymol. 2007; 425:241-62.
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Zhao X, Yu YT. Incorporation of 5-fluorouracil into U2 snRNA blocks pseudouridylation and pre-mRNA splicing in vivo. Nucleic Acids Res. 2007; 35(2):550-8.
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Yu YT. The most complex pseudouridylase. Structure. 2006 Feb; 14(2):167-8.
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Moon KH, Zhao X, Yu YT. Pre-mRNA splicing in the nuclei of Xenopus oocytes. Methods Mol Biol. 2006; 322:149-63.
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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. EMBO J. 2005 Jul 6; 24(13):2403-13.
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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. J Biol Chem. 2005 Feb 25; 280(8):6655-62.
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Zhao X, Yu YT. Detection and quantitation of RNA base modifications. RNA. 2004 Jun; 10(6):996-1002.
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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.
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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.
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Ma X, Zhao X, Yu YT. Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism. EMBO J. 2003 Apr 15; 22(8):1889-97.
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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.
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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. J Cell Biol. 2001 Mar 19; 152(6):1279-88.
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Yu YT. Site-specific 4-thiouridine incorporation into RNA molecules. Methods Enzymol. 2000; 318:71-88.
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Yu YT. Construction of 4-thiouridine site-specifically substituted RNAs for cross-linking studies. Methods. 1999 May; 18(1):13-21.
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Yu YT, Shu MD, Steitz JA. Modifications of U2 snRNA are required for snRNP assembly and pre-mRNA splicing. EMBO J. 1998 Oct 1; 17(19):5783-95.
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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.
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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.
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Yu YT, Steitz JA. Site-specific crosslinking of mammalian U11 and u6atac to the 5' splice site of an AT-AC intron. Proc Natl Acad Sci U S A. 1997 Jun 10; 94(12):6030-5.
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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.
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Yu YT, Tarn WY, Yario TA, Steitz JA. More Sm snRNAs from vertebrate cells. Exp Cell Res. 1996 Dec 15; 229(2):276-81.
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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.
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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.
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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.
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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.
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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.
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Yu YT, Nilsen TW. Sequence requirements for maturation of the 5' terminus of human 18 S rRNA in vitro. J Biol Chem. 1992 May 5; 267(13):9264-8.
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