Global analysis of yeast RNA processing identifies new targets of RNase III and uncovers a link between tRNA 5′ end processing and tRNA splicing

• Published in: Nucleic acids research Vol. 33; no. 9; pp. 3048 - 3056
• Main Authors: Hiley, Shawna L., Babak, Tomas, Hughes, Timothy R.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2005; Oxford Publishing Limited (England)
• Subjects: Gene Expression Regulation, Fungal; Oligonucleotide Array Sequence Analysis; Oligonucleotide Probes; Ribonuclease III - metabolism; RNA Processing, Post-Transcriptional; RNA Splicing; RNA, Small Nucleolar - metabolism; RNA, Transfer - metabolism; RNA, Untranslated - analysis; RNA, Untranslated - biosynthesis; RNA, Untranslated - metabolism; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - metabolism
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gki608

We used a microarray containing probes that tile all known yeast noncoding RNAs (ncRNAs) to investigate RNA biogenesis on a global scale. The microarray verified a general loss of Box C/D snoRNAs in the TetO7-BCD1 mutant, which had previously been shown for only a handful of snoRNAs. We also monitored the accumulation of improperly processed flank sequences of pre-RNAs in strains depleted for known RNA nucleases, including RNase III, Dbr1p, Xrn1p, Rat1p and components of the exosome and RNase P complexes. Among the hundreds of aberrant RNA processing events detected, two novel substrates of Rnt1p (the RUF1 and RUF3 snoRNAs) were identified. 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 applicability of microarray technology to the study of global analysis of ncRNA synthesis and provides an extensive directory of processing events mediated by yeast ncRNA processing enzymes.