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Nucleic Acids Research 2005 33(1):e2; doi:10.1093/nar/gni002
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Published online 7 January 2005

© 2005, the authors Nucleic Acids Research, Vol. 33 No. 1 © Oxford University Press 2005; all rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.

Methods Online

Detection and discovery of RNA modifications using microarrays

Shawna L. Hiley1, Jane Jackman2, Tomas Babak1,3, Miles Trochesset1, Quaid D. Morris1, Eric Phizicky2 and Timothy R. Hughes1,3,*

1 Banting and Best Department of Medical Research, University of Toronto 112 College Street, Toronto, ON M5G 1L6, Canada 2 Department of Biochemistry and Biophysics Box 712 University of Rochester School of Medicine Rochester, NY 14642, USA 3 Department of Medical Genetics and Microbiology, University of Toronto 1 King's College Circle, Toronto, ON, Canada

*To whom correspondence should be addressed. Tel: +1 416 946 8260; Fax: +1 416 978 8528; Email: t.hughes{at}utoronto.ca

Received October 15, 2004. Revised December 6, 2004. Accepted December 6, 2004.

Using a microarray that tiles all known yeast non-coding RNAs, we compared RNA from wild-type cells with RNA from mutants encoding known and putative RNA modifying enzymes. We show that at least five types of RNA modification (dihydrouridine, m1G, , m1A and ) catalyzed by 10 different enzymes (Trm1p, Trm5, Trm10p, Dus1p-Dus4p, Dim1p, Gcd10p and Gcd14p) can be detected by virtue of differential hybridization to oligonucleotides on the array that are complementary to the modified sites. Using this approach, we identified a previously undetected m1A modification in GlnCTG tRNA, the formation of which is catalyzed by the Gcd10/Gcd14 complex.


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