Abstract #28

Defining the yeast transcriptome. Albert Lee, Michal Ronen, Katja Schwartz, Gavin Sherlock. Department of Genetics, Stanford University, Stanford, CA.
   The budding yeast, Saccharomyces cerevisiae, is one of the most well studied and understood organisms, and as the first eukaryote to have its genome fully sequenced, it has served as a model system to study eukaryotic biology. However, even a decade after the 1996 release of its sequenced genome, we still do not know the location of all the genes within the genome. Currently, there are of hundreds of ORFs listed in SGD as being ‘dubious’, while there are likely many other genes in the genome that remain unrecognized, because there has not yet been a systematic effort to identify all transcripts encoded by the yeast genome. In order to address this issue, we are using a systematic and comprehensive approach, combining a carefully selected, diverse set of experimental conditions and high-density oligonucleotide microarrays in order to obtain a high-resolution primary annotation of the yeast transcriptome (to three nucleotide resolution). We are using systematic statistically robust analyses to differentiate transcribed regions of the genome from background noise, as well as comparative genomics, and experimental analysis and characterization to validate these newly discovered transcripts. Our preliminary data suggest that there are, at least hundreds of novel transcripts, and furthermore, confirm the existence of transcripts for about 60 percent of the genes previously annotated as dubious. Once we have the full parts list encoded by the yeast genome in hand, we will be able to fully explore yeast biology in truly comprehensive studies, and apply the lesson learned to other organisms.

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