Exploration of the RNase III dependent nuclear processing and degradation mechanisms of RNA in Saccharomyces cerevisiae

RNA molecules have had a very important role in living organisms, both past and present. Maintaining the integrity of RNA molecules through RNA surveillance is an essential process which involves a number of RNA endoribonucleases as well as RNA exoribonucleases. RNase III enzymes perform double-stranded RNA cleavage through which they assist in the processing and degradation of many types of RNA molecules. The S. cerevisiae ortholog of RNase III, Rnt1p, takes part in many of these processing events by cleaving noncoding RNAs such as rRNA, snRNAs and snoRNAs. Additionally, Rnt1p also takes part in RNA surveillance by facilitating the degradation of a number of noncoding RNAs as well as mRNAs and pre-mRNAs. Here we show that a number of cleavage intermediates of Rnt1p become 3' polyadenylated by RNA surveillance mechanisms involving the Trf4p poly(A) polymerase, and are subsequently further processed or degraded by the nuclear exosome. In addition, we show that the mating-type specific gene MATa1, expressed in MATa and in diploid cells, is regulated by nuclear RNA surveillance mechanisms. RNA forms resulting from variant splicing of the pre-MATa1 mRNA containing two introns are targeted for degradation through the 5' to 3' exonuclease Xrn1p and Rat1p, the RNase III endonuclease, and possibly the Nonsense Mediated Decay pathway. These novel examples of regulation through RNA processing and RNA decay underscore the importance of post-transcriptional processes in eukaryotic gene regulation.