Yi Tao Yu

Summary

Affiliation: University of Rochester
Country: USA

Publications

  1. pmc Internal modification of U2 small nuclear (sn)RNA occurs in nucleoli of Xenopus oocytes
    Y T Yu
    Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA
    J Cell Biol 152:1279-88. 2001
  2. pmc Targeted 2'-O methylation at a nucleotide within the pseudoknot of telomerase RNA reduces telomerase activity in vivo
    Chao Huang
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
    Mol Cell Biol 30:4368-78. 2010
  3. doi request reprint Pseudouridines in spliceosomal snRNAs
    Andrew T Yu
    Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
    Protein Cell 2:712-25. 2011
  4. doi request reprint Functions and mechanisms of spliceosomal small nuclear RNA pseudouridylation
    Guowei Wu
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
    Wiley Interdiscip Rev RNA 2:571-81. 2011
  5. pmc A flexible RNA backbone within the polypyrimidine tract is required for U2AF65 binding and pre-mRNA splicing in vivo
    Chun Chen
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
    Mol Cell Biol 30:4108-19. 2010
  6. pmc An H/ACA guide RNA directs U2 pseudouridylation at two different sites in the branchpoint recognition region in Xenopus oocytes
    Xinliang Zhao
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
    RNA 8:1515-25. 2002
  7. pmc Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism
    Xiaoju Ma
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
    EMBO J 22:1889-97. 2003
  8. ncbi request reprint Psi35 in the branch site recognition region of U2 small nuclear RNA is important for pre-mRNA splicing in Saccharomyces cerevisiae
    Chunxing Yang
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
    J Biol Chem 280:6655-62. 2005
  9. pmc RNA pseudouridylation: new insights into an old modification
    Junhui Ge
    Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
    Trends Biochem Sci 38:210-8. 2013
  10. ncbi request reprint Pre-mRNA splicing in the nuclei of Xenopus oocytes
    Kyong Hwa Moon
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
    Methods Mol Biol 322:149-63. 2006

Collaborators

  • J A Steitz
  • John Karijolich
  • Xinliang Zhao
  • Chao Huang
  • Junhui Ge
  • Guowei Wu
  • Chunxing Yang
  • Andrew T Yu
  • Athena Kantartzis
  • Mu Xiao
  • Xiaoju Ma
  • Chun Chen
  • Kyong Hwa Moon
  • Ryszard Kierzek
  • Huimin Liu
  • Peter Schattner
  • Andrei Alexandrov
  • Elizabeth J Grayhack
  • Isabelle Behm-Ansmant
  • David S McPheeters
  • Michael P Terns
  • Rebecca M Terns
  • Zhu Hong Li

Detail Information

Publications23

  1. pmc Internal modification of U2 small nuclear (sn)RNA occurs in nucleoli of Xenopus oocytes
    Y T Yu
    Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA
    J Cell Biol 152:1279-88. 2001
    ..Analysis of additional chimeric U2 RNAs reveals a correlation between internal modification and nucleolar localization. Together, our results suggest that U2 internal modification occurs within the nucleolus...
  2. pmc Targeted 2'-O methylation at a nucleotide within the pseudoknot of telomerase RNA reduces telomerase activity in vivo
    Chao Huang
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
    Mol Cell Biol 30:4368-78. 2010
    ..Our results demonstrate that RNA-guided RNA modification is a highly useful approach for modulating telomerase activity...
  3. doi request reprint Pseudouridines in spliceosomal snRNAs
    Andrew T Yu
    Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
    Protein Cell 2:712-25. 2011
    ....
  4. doi request reprint Functions and mechanisms of spliceosomal small nuclear RNA pseudouridylation
    Guowei Wu
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
    Wiley Interdiscip Rev RNA 2:571-81. 2011
    ..Experimental data also indicate that spliceosomal snRNA pseudouridylation can be catalyzed by both RNA-dependent (box H/ACA Ribonucleoproteins) and RNA-independent (protein-only enzymes) mechanisms...
  5. pmc A flexible RNA backbone within the polypyrimidine tract is required for U2AF65 binding and pre-mRNA splicing in vivo
    Chun Chen
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
    Mol Cell Biol 30:4108-19. 2010
    ..This pseudouridine effect can also be applied to other pre-mRNA polypyrimidine tracts. Thus, our work demonstrates that in vivo binding of U2AF(65) to a polypyrimidine tract requires a flexible RNA backbone...
  6. pmc An H/ACA guide RNA directs U2 pseudouridylation at two different sites in the branchpoint recognition region in Xenopus oocytes
    Xinliang Zhao
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
    RNA 8:1515-25. 2002
    ..Our results clarify the mechanism of U2 snRNA pseudouridylation in Xenopus oocytes, and have interesting implications with regard to the intranuclear localization of U2 snRNA pseudouridylation...
  7. pmc Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism
    Xiaoju Ma
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
    EMBO J 22:1889-97. 2003
    ..A BLAST search revealed Pus7 homologs in various organisms...
  8. ncbi request reprint Psi35 in the branch site recognition region of U2 small nuclear RNA is important for pre-mRNA splicing in Saccharomyces cerevisiae
    Chunxing Yang
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
    J Biol Chem 280:6655-62. 2005
    ....
  9. pmc RNA pseudouridylation: new insights into an old modification
    Junhui Ge
    Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
    Trends Biochem Sci 38:210-8. 2013
    ....
  10. ncbi request reprint Pre-mRNA splicing in the nuclei of Xenopus oocytes
    Kyong Hwa Moon
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
    Methods Mol Biol 322:149-63. 2006
    ..g., mutant snRNAs, snRNAs with or without modified nucleotides) can be constructed readily, the results obtained from this procedure provide valuable information on the function of a particular snRNA of interest in pre-mRNA splicing...
  11. pmc Regulation of pre-mRNA splicing in Xenopus oocytes by targeted 2'-O-methylation
    Junhui Ge
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
    RNA 16:1078-85. 2010
    ..Our results demonstrate that RNA-guided pre-mRNA modification can occur in the nucleoplasm of vertebrate cells, thus offering a powerful tool for molecular biology research...
  12. pmc U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP
    Guowei Wu
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
    EMBO J 30:79-89. 2011
    ..Our results thus demonstrate for the first time that pseudouridylation of RNA can be induced at sites of imperfect sequences, and that Pus7p and snR81 RNP can catalyse both constitutive and inducible pseudouridylation...
  13. ncbi request reprint Spliceosomal snRNA modifications and their function
    John Karijolich
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
    RNA Biol 7:192-204. 2010
    ..The role of spliceosomal snRNA modifications in snRNP biogenesis and spliceosome assembly has also been verified...
  14. pmc Detection and quantitation of RNA base modifications
    Xinliang Zhao
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
    RNA 10:996-1002. 2004
    ..With minor modifications, this method can serve as an effective assay to study RNA modifying enzymes...
  15. pmc Pseudouridylation of yeast U2 snRNA is catalyzed by either an RNA-guided or RNA-independent mechanism
    Xiaoju Ma
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
    EMBO J 24:2403-13. 2005
    ..Our data indicate that snRNA pseudouridylation can be catalyzed by both RNA-dependent and RNA-independent mechanisms...
  16. doi request reprint Quantitative analysis of RNA modifications
    John Karijolich
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
    Methods Mol Biol 629:21-32. 2010
    ..This procedure involves a number of techniques, including oligonucleotide-affinity selection, site-specific cleavage and radiolabeling, nuclease digestion, and thin layer chromatography...
  17. pmc Inducing nonsense suppression by targeted pseudouridylation
    Chao Huang
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, USA
    Nat Protoc 7:789-800. 2012
    ..Thus, the experimental procedures described in this protocol may provide a novel way to treat PTC-related diseases. This protocol takes 10-13 d to complete...
  18. doi request reprint RNA modifications: a mechanism that modulates gene expression
    John Karijolich
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
    Methods Mol Biol 629:1-19. 2010
    ..In this chapter, we highlight the functional aspects of the modifications of spliceosomal snRNA and rRNA and provide a framework for understanding how posttranscriptional modifications are capable of influencing gene expression...
  19. pmc Converting nonsense codons into sense codons by targeted pseudouridylation
    John Karijolich
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, USA
    Nature 474:395-8. 2011
    ..Our results also suggest that RNA modification, as a naturally occurring mechanism, may offer a new way to expand the genetic code...
  20. doi request reprint Post-transcriptional modification of RNAs by artificial Box H/ACA and Box C/D RNPs
    Chao Huang
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
    Methods Mol Biol 718:227-44. 2011
    ..Here, we present strategies for constructing guide RNAs and manipulating RNA modifications in the nucleus...
  21. pmc Incorporation of 5-fluorouracil into U2 snRNA blocks pseudouridylation and pre-mRNA splicing in vivo
    Xinliang Zhao
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
    Nucleic Acids Res 35:550-8. 2007
    ..This mechanism may contribute substantially to 5FU-mediated cell death...
  22. ncbi request reprint Targeted pre-mRNA modification for gene silencing and regulation
    Xinliang Zhao
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, USA
    Nat Methods 5:95-100. 2008
    ..We targeted other essential intron-containing genes, and observed a similar phenotype. We demonstrated that a Box C/D RNA can guide modification at the pre-mRNA branch point, thus silencing its expression and inducing cell death...
  23. pmc Functionality and substrate specificity of human box H/ACA guide RNAs
    Mu Xiao
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
    RNA 15:176-86. 2009
    ..We found that the predictions of one program (snoGPS) agreed with our experimental results with 100% sensitivity (12/12) and 75% specificity (3/4)...

Research Grants11

  1. Targeted pre-mRNA modification and gene silencing
    Yi Tao Yu; Fiscal Year: 2007
    ..We believe that our novel method will prove effective and useful in mammalian systems as well as in yeast. ..
  2. Spliceosomal snRNA modification in Xenopus oocytes
    Yi Tao Yu; Fiscal Year: 2007
    ..Identification of mRNA/pre- mRNA modifications will form the basis for future functional analyses. ..
  3. Spliceosomal snRNA modification in Xenopus oocytes
    Yi Tao Yu; Fiscal Year: 2005
    ..We will use a variety of biochemical approaches to search for such putative guide RNAs and to identify the modifying activity responsible for 2'-O-methylation and pseudouridylation. ..
  4. Spliceosomal snRNA modification in Xenopus oocytes
    Yi Tao Yu; Fiscal Year: 2009
    ..Identification of mRNA/pre- mRNA modifications will form the basis for future functional analyses. ..