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Yi-Tao Yu, Ph.D.

Yi-Tao Yu, Ph.D.

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About Me

Faculty Appointments

Professor - Department of Biochemistry and Biophysics (SMD)

Dean's Professorship - Department of Biochemistry and Biophysics (SMD)

Credentials

Education

PhD | Case Western Reserve University. Molecular Biology. 1994

MS | Shanghai Institute of Physiology, Chinese Academy of Sciences. Neurobiology. 1988

BS | Fudan University. Chemistry. 1982

Post-doctoral training | Department of Molecular Biophysics & Biochemistry, HHMI, Yale University School of Medicine. Molecular Biology. 0

Research

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 p...
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.

Patents

Nonsense Suppression and Genetic Codon Alteration by Targeted Modification

Issue date: December 10, 2013

Patent #: 8,603,457

Country: United States

Inventors: Yi-Tao Yu, Xinliang Zhao

Targeted 2'-O-Methylation of Telomerase Non-Coding RNA

Issue date: March 01, 2016

Patent #: 9,273,294

Country: United States

Inventors: Chao Huang, Yi-Tao Yu

Targeted Pre-mRNA/mRNA Modification and Gene Regulation

Issue date: January 19, 2016

Patent #: 9,238,813

Country: United States

Inventors: Yi-Tao Yu, Xinliang Zhao

Publications

Journal Articles

Therapeutic Nonsense Suppression Modalities: From Small Molecules to Nucleic Acid-Based Approaches.

Morais P, Zhang R, Yu YT

Biomedicines.. 2024 June 1012 (6)Epub 06/10/2024.

Updated Pseudo-seq Protocol for Transcriptome-Wide Detection of Pseudouridines.

Pan Y, Adachi H, He X, Chen JL, Yu YT, Boutz PL

Bio-protocol.. 2024 May 514 (9):e4985. Epub 05/05/2024.

Pseudouridylation-mediated gene expression modulation.

Chen JL, Leeder WM, Morais P, Adachi H, Yu YT

The Biochemical journal.. 2024 January 10481 (1):1-16. Epub 1900 01 01.

Targeted pseudouridylation: An approach for suppressing nonsense mutations in disease genes.

Adachi H, Pan Y, He X, Chen JL, Klein B, Platenburg G, Morais P, Boutz P, Yu YT

Molecular cell.. 2023 February 1683 (4):637-651.e9. Epub 02/09/2023.

In Vitro Reconstitution of Pseudouridylation Catalyzed by Human Box H/ACA Ribonucleoprotein Particles.

Adachi H, Chen JL, Yin Q, Morais P, Yu YT

Methods in molecular biology.. 2023 2666 :177-191. Epub 1900 01 01.

From Antisense RNA to RNA Modification: Therapeutic Potential of RNA-Based Technologies.

Adachi H, Hengesbach M, Yu YT, Morais P

Biomedicines.. 2021 May 149 (5)Epub 05/14/2021.

Spliceosomal snRNA Epitranscriptomics.

Morais P, Adachi H, Yu YT

Frontiers in genetics.. 2021 12 :652129. Epub 03/02/2021.

The Critical Contribution of Pseudouridine to mRNA COVID-19 Vaccines.

Morais P, Adachi H, Yu YT

Frontiers in cell and developmental biology.. 2021 9 :789427. Epub 11/04/2021.

Pseudouridine-mediated stop codon readthrough in is sequence context-independent.

Adachi H, Yu YT

RNA.. 2020 September 26 (9):1247-1256. Epub 05/20/2020.

Suppression of Nonsense Mutations by New Emerging Technologies.

Morais P, Adachi H, Yu YT

International journal of molecular sciences.. 2020 June 2021 (12)Epub 06/20/2020.

Post-transcriptional pseudouridylation in mRNA as well as in some major types of noncoding RNAs.

Adachi H, De Zoysa MD, Yu YT

Biochimica et biophysica acta. Gene regulatory mechanisms.. 2019 March 1862 (3):230-239. Epub 11/08/2018.

Detection and Quantification of Pseudouridine in RNA.

Adachi H, DeZoysa MD, Yu YT

Methods in molecular biology.. 2019 1870 :219-235. Epub 1900 01 01.

Guide-substrate base-pairing requirement for box H/ACA RNA-guided RNA pseudouridylation.

De Zoysa MD, Wu G, Katz R, Yu YT

RNA.. 2018 August 24 (8):1106-1117. Epub 06/05/2018.

The Role of Noncoding RNA Pseudouridylation in Nuclear Gene Expression Events.

Zhao Y, Dunker W, Yu YT, Karijolich J

Frontiers in bioengineering and biotechnology.. 2018 6 :8. Epub 02/08/2018.

5-Fluorouracil Treatment Alters the Efficiency of Translational Recoding.

Ge J, Karijolich J, Zhai Y, Zheng J, Yu YT

Genes.. 2017 October 318 (11)Epub 10/31/2017.

Regulatory RNPs: a novel class of ribonucleoproteins that potentially contribute to ribosome heterogeneity.

Poole AR, Vicino I, Adachi H, Yu YT, Hebert MD

Biology open.. 2017 September 156 (9):1342-1354. Epub 09/15/2017.

Posttranscriptional RNA Pseudouridylation.

De Zoysa MD, Yu YT

The Enzymes.. 2017 41 :151-167. Epub 03/11/2017.

Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly.

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

Genes & development.. 2016 November 130 (21):2376-2390. Epub 11/10/2016.

The TOR signaling pathway regulates starvation-induced pseudouridylation of yeast U2 snRNA.

Wu G, Radwan MK, Xiao M, Adachi H, Fan J, Yu YT

RNA.. 2016 August 22 (8):1146-52. Epub 06/07/2016.

Detection and quantification of RNA 2'-O-methylation and pseudouridylation.

Huang C, Karijolich J, Yu YT

Methods : a companion to Methods in enzymology.. 2016 July 1103 :68-76. Epub 02/04/2016.

Pseudouridines in U2 snRNA stimulate the ATPase activity of Prp5 during spliceosome assembly.

Wu G, Adachi H, Ge J, Stephenson D, Query CC, Yu YT

The EMBO journal.. 2016 March 1535 (6):654-67. Epub 02/12/2016.

Purification and Functional Reconstitution of Box H/ACA Ribonucleoprotein Particles.

Huang C, Wu G, Yu YT

Methods in molecular biology.. 2016 1421 :97-109. Epub 1900 01 01.

Transcriptome-wide dynamics of RNA pseudouridylation.

Karijolich J, Yi C, Yu YT

Nature reviews. Molecular cell biology.. 2015 October 16 (10):581-5. Epub 08/19/2015.

The new era of RNA modification.

Karijolich J, Yu YT

RNA.. 2015 April 21 (4):659-60. Epub 1900 01 01.

Cajal body proteins differentially affect the processing of box C/D scaRNPs.

Enwerem II, Wu G, Yu YT, Hebert MD

PloS one.. 2015 10 (4):e0122348. Epub 04/13/2015.

Pseudouridine in mRNA: Incorporation, Detection, and Recoding.

Wu G, Huang C, Yu YT

Methods in enzymology.. 2015 560 :187-217. Epub 04/27/2015.

Insight into the mechanisms and functions of spliceosomal snRNA pseudouridylation.

Adachi H, Yu YT

World journal of biological chemistry. 2014 November 265 (4):398-408. Epub 1900 01 01.

Therapeutic suppression of premature termination codons: mechanisms and clinical considerations (review).

Karijolich J, Yu YT

International journal of molecular medicine.. 2014 August 34 (2):355-62. Epub 06/17/2014.

Purification of radiolabeled RNA products using denaturing gel electrophoresis.

Adachi H, Yu YT

Current protocols in molecular biology. 2014 January 6105 :Unit 4.20.. Epub 01/06/2014.

Requirement for CRIF1 in RNA interference and Dicer-2 stability.

Jun Lim S, Scott A, Xiong XP, Vahidpour S, Karijolich J, Guo D, Pei S, Yu YT, Zhou R, Li W

RNA biology.. 2014 11 (9):1171-9. Epub 1900 01 01.

RNA-guided isomerization of uridine to pseudouridine--pseudouridylation.

Yu YT, Meier UT

RNA biology.. 2014 11 (12):1483-94. Epub 1900 01 01.

Unusual base pairing during the decoding of a stop codon by the ribosome.

Fernández IS, Ng CL, Kelley AC, Wu G, Yu YT, Ramakrishnan V

Nature.. 2013 August 1500 (7460):107-10. Epub 06/30/2013.

RNA pseudouridylation: new insights into an old modification.

Ge J, Yu YT

Trends in biochemical sciences.. 2013 April 38 (4):210-8. Epub 02/04/2013.

Synthesis and labeling of RNA in vitro.

Huang C, Yu YT

Current protocols in molecular biology. 2013 April Chapter 4 :Unit4.15. Epub 1900 01 01.

Synthesis and labeling of RNA in vitro.

Huang, C; Yu, YT.

Wiley Current Protocols in Molecular Biology. 2013; .

Inducing nonsense suppression by targeted pseudouridylation.

Huang C, Wu G, Yu YT

Nature protocols.. 2012 March 297 (4):789-800. Epub 03/29/2012.

Inducing nonsense suppression by targeted pseudouridylation.

Huang, C; Wu, G; Yu, YT.

Nature Protocols. 2012; 7: 789-800.

Pseudouridines in spliceosomal snRNAs.

Yu AT, Ge J, Yu YT

Protein & cell.. 2011 September 2 (9):712-25. Epub 10/06/2011.

Converting nonsense codons into sense codons by targeted pseudouridylation.

Karijolich J, Yu YT

Nature.. 2011 June 15474 (7351):395-8. Epub 06/15/2011.

U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP.

Wu G, Xiao M, Yang C, Yu YT

The EMBO journal.. 2011 January 530 (1):79-89. Epub 12/03/2010.

Functions and Mechanisms of Spliceosomal snRNA pseudouridylation.

Wu G; Yu AT; Kantartzis A; Yu YT.

Wiley Interdisciplinary Reviews (WIREs) RNA. 2011; 2: 571-581.

Pseudouridines in spliceosomal snRNAs.

Yu, AT; Ge, J; Yu, YT.

Protein & Cell. 2011; 2: 712-725.

Post-transcriptional modification of RNAs by artificial Box H/ACA and Box C/D RNPs.

Huang C, Karijolich J, Yu YT

Methods in molecular biology.. 2011 718 :227-44. Epub 1900 01 01.

Functions and mechanisms of spliceosomal small nuclear RNA pseudouridylation.

Wu G, Yu AT, Kantartzis A, Yu YT

Wiley interdisciplinary reviews. RNA.. 2011 2 (4):571-81. Epub 02/18/2011.

A flexible RNA backbone within the polypyrimidine tract is required for U2AF65 binding and pre-mRNA splicing in vivo.

Chen C, Zhao X, Kierzek R, Yu YT

Molecular and cellular biology.. 2010 September 30 (17):4108-19. Epub 07/06/2010.

Targeted 2'-O methylation at a nucleotide within the pseudoknot of telomerase RNA reduces telomerase activity in vivo.

Huang C, Yu YT

Molecular and cellular biology.. 2010 September 30 (18):4368-78. Epub 07/20/2010.

Regulation of pre-mRNA splicing in Xenopus oocytes by targeted 2'-O-methylation.

Ge J, Liu H, Yu YT

RNA.. 2010 May 16 (5):1078-85. Epub 03/26/2010.

Spliceosomal snRNA modifications and their function.

Karijolich J, Yu YT

RNA biology.. 2010 7 (2):192-204. Epub 03/14/2010.

RNA modifications: a mechanism that modulates gene expression.

Karijolich J, Kantartzis A, Yu YT

Methods in molecular biology.. 2010 629 :1-19. Epub 1900 01 01.

Quantitative analysis of RNA modifications.

Karijolich J, Kantartzis A, Yu YT

Methods in molecular biology.. 2010 629 :21-32. Epub 1900 01 01.

Functionality and substrate specificity of human box H/ACA guide RNAs.

Xiao M, Yang C, Schattner P, Yu YT

RNA.. 2009 January 15 (1):176-86. Epub 11/25/2008.

Spliceosomal snRNA pseudouridylation.

Karijolich, J; Huang, C; Yu, YT.

In DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution (ed. H. Grosjean). Landes Bioscience. 2009; : 461-474.

Insight into the Protein Components of the Box H/ACA RNP.

Karijolich J, Yu YT

Current proteomics. 2008 July 15 (2):129-137. Epub 1900 01 01.

Targeted pre-mRNA modification for gene silencing and regulation.

Zhao X, Yu YT

Nature methods.. 2008 January 5 (1):95-100. Epub 12/09/2007.

Functional roles of spliceosomal snRNA modifications in pre-mRNA splicing.

Stephenson, D; Karijolich, J; Yu, YT.

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.

Pre-mRNA splicing

Karijolich, J.; Yu, Y.T.;.

Wiley Encyclopedia of Chemical Biology. (ed. TP Begley). 2007; : DOI: 10.1002/9780470048672.wecb520. Article Online Posting.

Incorporation of 5-fluorouracil into U2 snRNA blocks pseudouridylation and pre-mRNA splicing in vivo.

Zhao X, Yu YT

Nucleic acids research.. 2007 35 (2):550-8. Epub 12/14/2006.

Biochemical purification of box H/ACA RNPs involved in pseudouridylation.

Karijolich J, Stephenson D, Yu YT

Methods in enzymology.. 2007 425 :241-62. Epub 1900 01 01.

Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine.

Dai Q, Fong R, Saikia M, Stephenson D, Yu YT, Pan T, Piccirilli JA

Nucleic acids research.. 2007 35 (18):6322-9. Epub 09/18/2007.

The most complex pseudouridylase.

Yu YT

Structure.. 2006 February 14 (2):167-8. Epub 1900 01 01.

Pre-mRNA splicing in the nuclei of Xenopus oocytes.

Moon KH, Zhao X, Yu YT

Methods in molecular biology.. 2006 322 :149-63. Epub 1900 01 01.

Pseudouridylation of yeast U2 snRNA is catalyzed by either an RNA-guided or RNA-independent mechanism.

Ma X, Yang C, Alexandrov A, Grayhack EJ, Behm-Ansmant I, Yu YT

The EMBO journal.. 2005 July 624 (13):2403-13. Epub 06/16/2005.

Psi35 in the branch site recognition region of U2 small nuclear RNA is important for pre-mRNA splicing in Saccharomyces cerevisiae.

Yang C, McPheeters DS, Yu YT

The Journal of biological chemistry.. 2005 February 25280 (8):6655-62. Epub 12/20/2004.

Mechanisms and functions of RNA-guided RNA modifications

Yu, Y.-T.; Terns, R. M.; Terns, M. P.;.

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.

Detection and quantitation of RNA base modifications.

Zhao X, Yu YT

RNA.. 2004 June 10 (6):996-1002. Epub 1900 01 01.

Pseudouridines in and near the branch site recognition region of U2 snRNA are required for snRNP biogenesis and pre-mRNA splicing in Xenopus oocytes.

Zhao X, Yu YT

RNA.. 2004 April 10 (4):681-90. Epub 1900 01 01.

The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Psi-synthase also acting on tRNAs.

Behm-Ansmant I, Urban A, Ma X, Yu YT, Motorin Y, Branlant C

RNA.. 2003 November 9 (11):1371-82. Epub 1900 01 01.

Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism.

Ma X, Zhao X, Yu YT

The EMBO journal.. 2003 April 1522 (8):1889-97. Epub 1900 01 01.

An H/ACA guide RNA directs U2 pseudouridylation at two different sites in the branchpoint recognition region in Xenopus oocytes.

Zhao X, Li ZH, Terns RM, Terns MP, Yu YT

RNA.. 2002 December 8 (12):1515-25. Epub 1900 01 01.

Internal modification of U2 small nuclear (sn)RNA occurs in nucleoli of Xenopus oocytes.

Yu YT, Shu MD, Narayanan A, Terns RM, Terns MP, Steitz JA

The Journal of cell biology.. 2001 March 19152 (6):1279-88. Epub 1900 01 01.

Site-specific 4-thiouridine incorporation into RNA molecules.

Yu YT

Methods in enzymology.. 2000 318 :71-88. Epub 1900 01 01.

Construction of 4-thiouridine site-specifically substituted RNAs for cross-linking studies.

Yu YT

Methods : a companion to Methods in enzymology.. 1999 May 18 (1):13-21. Epub 1900 01 01.

The growing world of small nuclear ribonucleoprotein particles

Yu, Y.T.; Scharl, E.C.; Smith, C.M.; Steitz, J.A. ;.

In The RNA World, 2nd edition (eds. Gesteland, Cech, and Atkins),Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. 1999; : 487-524.

Modifications of U2 snRNA are required for snRNP assembly and pre-mRNA splicing.

Yu YT, Shu MD, Steitz JA

The EMBO journal.. 1998 October 117 (19):5783-95. Epub 1900 01 01.

The position of site-directed cleavage of RNA using RNase H and 2'-O-methyl oligonucleotides is dependent on the enzyme source.

Lapham J, Yu YT, Shu MD, Steitz JA, Crothers DM

RNA.. 1997 September 3 (9):950-1. Epub 1900 01 01.

A new strategy for introducing photoactivatable 4-thiouridine ((4S)U) into specific positions in a long RNA molecule.

Yu YT, Steitz JA

RNA.. 1997 July 3 (7):807-10. Epub 1900 01 01.

Site-specific crosslinking of mammalian U11 and u6atac to the 5' splice site of an AT-AC intron.

Yu YT, Steitz JA

Proceedings of the National Academy of Sciences of the United States of America.. 1997 June 1094 (12):6030-5. Epub 1900 01 01.

A new method for detecting sites of 2'-O-methylation in RNA molecules.

Yu YT, Shu MD, Steitz JA

RNA.. 1997 March 3 (3):324-31. Epub 1900 01 01.

More Sm snRNAs from vertebrate cells.

Yu YT, Tarn WY, Yario TA, Steitz JA

Experimental cell research.. 1996 December 15229 (2):276-81. Epub 1900 01 01.

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.

Maroney PA, Yu YT, Jankowska M, Nilsen TW

RNA.. 1996 August 2 (8):735-45. Epub 1900 01 01.

Multiple requirements for nematode spliced leader RNP function in trans-splicing.

Denker JA, Maroney PA, Yu YT, Kanost RA, Nilsen TW

RNA.. 1996 August 2 (8):746-55. Epub 1900 01 01.

U6 snRNA function in nuclear pre-mRNA splicing: a phosphorothioate interference analysis of the U6 phosphate backbone.

Yu YT, Maroney PA, Darzynkiwicz E, Nilsen TW

RNA.. 1995 March 1 (1):46-54. Epub 1900 01 01.

Functional reconstitution of U6 snRNA in nematode cis- and trans-splicing: U6 can serve as both a branch acceptor and a 5' exon.

Yu YT, Maroney PA, Nilsen TW

Cell.. 1993 December 1775 (6):1049-59. Epub 1900 01 01.

Interaction of U6 snRNA with a sequence required for function of the nematode SL RNA in trans-splicing.

Hannon GJ, Maroney PA, Yu YT, Hannon GE, Nilsen TW

Science.. 1992 December 11258 (5089):1775-80. Epub 1900 01 01.

Sequence requirements for maturation of the 5' terminus of human 18 S rRNA in vitro.

Yu YT, Nilsen TW

The Journal of biological chemistry.. 1992 May 5267 (13):9264-8. Epub 1900 01 01.

Books

DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution (2009)

Chapter: Spliceosomal snRNA pseudouridylation

Authors: Karijolich, J., Huang, C. and Yu, Y.-T.

Publisher: Landes Bioscience, Austin, Texas 2009

RNA and DNA Editing: Molecular Mechanisms and Their Integration into Biological (2008)

Chapter: Functional roles of spliceosomal snRNA modifications in pre-mRNA splicing

Authors: Stephenson, D., Karijolich, J. and Yu, Y.-T.

Publisher: John Wiley & Sons Press, Hoboken, New Jersey 2008