Detection and discovery of RNA modifications using microarrays
Open Access
- 7 January 2005
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 33 (1) , e2
- https://doi.org/10.1093/nar/gni002
Abstract
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, m2(2)G, m1A and m6(2)A) 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. complex.Keywords
This publication has 25 references indexed in Scilit:
- The Specificities of Four Yeast Dihydrouridine Synthases for Cytoplasmic tRNAsJournal of Biological Chemistry, 2004
- A Panoramic View of Yeast Noncoding RNA ProcessingCell, 2003
- Pseudouridylation (Psi) of U2 snRNA in S.cerevisiae is catalyzed by an RNA-independent mechanismThe EMBO Journal, 2003
- The expanding snoRNA worldBiochimie, 2002
- Ribosomal RNA pseudouridines and pseudouridine synthasesFEBS Letters, 2002
- AdoMet-dependent methylation, DNA methyltransferases and base flippingNucleic Acids Research, 2001
- RNA editing by base deamination: more enzymes, more targets, new mysteriesTrends in Biochemical Sciences, 2001
- Ribosome Synthesis in Saccharomyces cerevisiaeAnnual Review of Genetics, 1999
- Compilation of tRNA sequences and sequences of tRNA genesNucleic Acids Research, 1998
- Crystallographic refinement of yeast aspartic acid transfer RNAJournal of Molecular Biology, 1985