Detection and discovery of RNA modifications using microarrays

Using a microarray that tiles all known yeast noncoding 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, m(1)G, m(2)(2)G, m(1)A and m(2)(6)A) catalyzed by 10 different enzymes (Trm1p, Trm5, Trm10p, Dus1p-Dus4p, Dim1p, Gcd10pand 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 m 1 A modification in GlnCTG tRNA, the formation of which is catalyzed by the Gcd10/Gcd14 complex.