Global analysis of yeast RNA processing by microarray identifies new targets of Rnase III and uncovers a link between tRNA 5' end processing

and tRNA splicing

 

 

Shawna L. Hiley¹, Tomas Babak^1,2 and Timothy R. Hughes^{1,2 §}

 

¹Banting and Best Department of Medical Research, University of Toronto, 112 College St., Toronto, ON M5G 1L6

 

²Department of Medical Genetics and Microbiology, University of Toronto, 1 King’s College Circle, Toronto, ON

 

 

^§To whom correspondence should be addressed:

t.hughes@utoronto.ca

phone: 416-946-8260

FAX: 416-978-8528

 

Abstract

We used a microarray that tiles all known yeast noncoding RNAs to investigate RNA biogenesis on a global scale. We verified a general loss of Box C/D snoRNAs in the tet-BCD1 mutant, relative to Box H/ACA snoRNAs, which had previously been shown for only a handful of snoRNAs. We also monitored accumulation of improperly processed flank sequences in strains depleted for known RNA nucleases, including RNaseIII, Dbr1, Xrn1, Rat1, and components of the exosome and RNaseP complexes. Among the hundreds of aberrant RNA processing events detected, we identified two novel substrates of Rnt1p (the RUF1 and RUF3 snoRNAs). We also identified a relationship between tRNA 5’ end processing and tRNA splicing, processes that were previously thought to be independent. This analysis demonstrates the general applicability of microarray technology to the study of noncoding RNA synthesis, and provides an extensive directory of processing events mediated by the general yeast noncoding RNA processing enzymes.