The study presents a novel RNA-Seq method for mapping the transcriptional landscape of the yeast genome. RNA-Seq involves sequencing cDNA fragments generated from poly(A) RNA, followed by computational mapping to the genome to identify transcribed regions. This method allows high-resolution mapping of the yeast transcriptome, revealing that 74.5% of the yeast genome is transcribed. The study confirms many known and predicted introns, identifies alternative initiation codons, and demonstrates the presence of upstream open reading frames (uORFs) in many yeast genes. It also reveals unexpected 3' end heterogeneity and the presence of many overlapping genes. RNA-Seq is shown to be at least as accurate as DNA microarrays for quantifying RNA expression levels and has a much larger dynamic range. The study also maps 5' and 3' boundaries of genes, confirming previously known introns and identifying new ones. RNA-Seq provides a comprehensive view of the yeast genome, revealing many novel transcribed regions not identified by other methods. The results indicate that the yeast transcriptome is more complex than previously appreciated. The study also demonstrates that RNA-Seq can accurately quantify gene expression levels and has a superior dynamic range compared to DNA microarrays. The findings highlight the importance of RNA-Seq in gene discovery and genome annotation, and suggest that many yeast genes contain uORFs that may regulate their downstream genes. The study also reveals that a large number of yeast genes have overlapping 3' ends, suggesting potential for gene regulation through overlapping transcription. Overall, the study provides a detailed and accurate map of the yeast genome, revealing new insights into gene structure and transcriptional regulation.The study presents a novel RNA-Seq method for mapping the transcriptional landscape of the yeast genome. RNA-Seq involves sequencing cDNA fragments generated from poly(A) RNA, followed by computational mapping to the genome to identify transcribed regions. This method allows high-resolution mapping of the yeast transcriptome, revealing that 74.5% of the yeast genome is transcribed. The study confirms many known and predicted introns, identifies alternative initiation codons, and demonstrates the presence of upstream open reading frames (uORFs) in many yeast genes. It also reveals unexpected 3' end heterogeneity and the presence of many overlapping genes. RNA-Seq is shown to be at least as accurate as DNA microarrays for quantifying RNA expression levels and has a much larger dynamic range. The study also maps 5' and 3' boundaries of genes, confirming previously known introns and identifying new ones. RNA-Seq provides a comprehensive view of the yeast genome, revealing many novel transcribed regions not identified by other methods. The results indicate that the yeast transcriptome is more complex than previously appreciated. The study also demonstrates that RNA-Seq can accurately quantify gene expression levels and has a superior dynamic range compared to DNA microarrays. The findings highlight the importance of RNA-Seq in gene discovery and genome annotation, and suggest that many yeast genes contain uORFs that may regulate their downstream genes. The study also reveals that a large number of yeast genes have overlapping 3' ends, suggesting potential for gene regulation through overlapping transcription. Overall, the study provides a detailed and accurate map of the yeast genome, revealing new insights into gene structure and transcriptional regulation.