Global analysis of yeast RNA processing identifies new targets of RNase III and uncovers a link between tRNA 5' end processing and tRNA splicing.
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.
Hiley
Shawna L
SL
Banting and Best Department of Medical Research, University of Toronto 112 College Street, Toronto, ON M5G 1L6, Canada.
Babak
Tomas
T
Hughes
Timothy R
TR
D015966:Gene Expression Regulation, Fungal; D020411:Oligonucleotide Array Sequence Analysis; D015345:Oligonucleotide Probes; D012323:RNA Processing, Post-Transcriptional; D012326:RNA Splicing; D020537:RNA, Small Nucleolar / Q000378:metabolism; D012343:RNA, Transfer / Q000378:metabolism*; D022661:RNA, Untranslated / Q000032:analysis / Q000096:biosynthesis / Q000378:metabolism*; D043244:Ribonuclease III / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*
D015345:Oligonucleotide Probes; D020537:RNA, Small Nucleolar; D022661:RNA, Untranslated; D029701:Saccharomyces cerevisiae Proteins; D012343:RNA, Transfer; C468367:RNT1 protein, S cerevisiae; D043244:Ribonuclease III