title: The transcriptional landscape of the yeast genome defined by RNA sequencing.
abstract: The identification of untranslated regions, introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome. We applied RNA-Seq to generate a high-resolution transcriptome map of the yeast genome and 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 also were 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.
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.
authors.forename: Ugrappa
authors.initials: U
authors.lastname: Nagalakshmi
authors.forename: Zhong
authors.initials: Z
authors.lastname: Wang
authors.forename: Karl
authors.initials: K
authors.lastname: Waern
authors.forename: Chong
authors.initials: C
authors.lastname: Shou
authors.forename: Debasish
authors.initials: D
authors.lastname: Raha
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
mesh_terms: D000465:Algorithms; D018387:Codon, Initiator; D019295:Computational Biology; D018076:DNA, Complementary; D021901:DNA, Intergenic; D020869:Gene Expression Profiling; D005800:Genes, Fungal; D016681:Genome, Fungal; D023281:Genomics; D007438:Introns; D016366:Open Reading Frames; D012331:RNA, Fungal / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic; D020506:Untranslated Regions
chemical_list: D018387:Codon, Initiator; D018076:DNA, Complementary; D021901:DNA, Intergenic; D012331:RNA, Fungal; D020506:Untranslated Regions