The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

The identification of untranslated regions (UTRs), introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq in which cDNA fragments are subjected to high throughput sequencing. We applied RNA-Seq to generate a high-resolution transcriptome map of the yeast genomeand demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed. We confirmed many known and predicted introns and demonstrated that others are not actively used. Alternative initiation codons and upstream open reading frames were also identified for many yeast genes. We also found unexpected 3' end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated. Keywords: RNA-Seq, mRNA expression profiling, Illumina high-throughput sequencing Oligo(dT) primed dataset has one technical and one biological replicates (total 3), Random Hexamer primed dataset has one technical and one biological replicates (total 3).