|
1
|
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; 35:6322-9. [PMID: 17881375 PMCID: PMC2094055 DOI: 10.1093/nar/gkm657] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Over 100 chemical types of RNA modifications have been identified in thousands of sites in all three domains of life. Recent data suggest that modifications function synergistically to mediate biological function, and that cells may coordinately modulate modification levels for regulatory purposes. However, this area of RNA biology remains largely unexplored due to the lack of robust, high-throughput methods to quantify the extent of modification at specific sites. Recently, we developed a facile enzymatic ligation-based method for detection and quantitation of methylated 2′-hydroxyl groups within RNA. Here we exploit the principles of molecular recognition and nucleic acid chemistry to establish the experimental parameters for ligation-based detection and quantitation of pseudouridine (Ψ) and N6-methyladenosine (m6A), two abundant modifications in eukaryotic rRNA/tRNA and mRNA, respectively. Detection of pseudouridylation at several sites in the large subunit rRNA derived from yeast demonstrates the feasibility of the approach for analysis of pseudouridylation in biological RNA samples.
Collapse
Affiliation(s)
- Qing Dai
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Robert Fong
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Mridusmita Saikia
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - David Stephenson
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Yi-tao Yu
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Joseph A. Piccirilli
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
- *To whom correspondence should be addressed. +1 773 702 9312+1 773 702 0271 Correspondence may also be addressed to Tao Pan. +1 773 702 4179+1 773 702 0439; E-mail:
| |
Collapse
|