A complete description of the transcriptome of an organism is crucial for a 
comprehensive understanding of how it functions and how its transcriptional 
networks are controlled, and may provide insights into the organism's evolution. 
Despite the status of Saccharomyces cerevisiae as arguably the most well-studied 
model eukaryote, we still do not have a full catalog or understanding of all its 
genes. In order to interrogate the transcriptome of S. cerevisiae for low 
abundance or rapidly turned over transcripts, we deleted elements of the RNA 
degradation machinery with the goal of preferentially increasing the relative 
abundance of such transcripts. We then used high-resolution tiling microarrays 
and ultra high-throughput sequencing (UHTS) to identify, map, and validate 
unannotated transcripts that are more abundant in the RNA degradation mutants 
relative to wild-type cells. We identified 365 currently unannotated 
transcripts, the majority presumably representing low abundance or short-lived 
RNAs, of which 185 are previously unknown and unique to this study. It is likely 
that many of these are cryptic unstable transcripts (CUTs), which are rapidly 
degraded and whose function(s) within the cell are still unclear, while others 
may be novel functional transcripts. Of the 185 transcripts we identified as 
novel to our study, greater than 80 percent come from regions of the genome that 
have lower conservation scores amongst closely related yeast species than 85 
percent of the verified ORFs in S. cerevisiae. Such regions of the genome have 
typically been less well-studied, and by definition transcripts from these 
regions will distinguish S. cerevisiae from these closely related species.