title: Genome-wide profiling of untranslated regions by paired-end ditag sequencing reveals unexpected transcriptome complexity in yeast.
abstract: The identification of structural and functional elements encoded in a genome is a challenging task. Although the transcriptome of budding yeast has been extensively analyzed, the boundaries and untranslated regions of yeast genes remain elusive. To address this least-explored field of yeast genomics, we performed a transcript profiling analysis through paired-end ditag (PET) approach coupled with deep sequencing. With 562,133 PET sequences we accurately defined the boundaries and untranslated regions of 3,409 ORFs, suggesting many yeast genes have multiple transcription start sites (TSSs). We also identified 85 previously uncharacterized transcripts either in intergenic regions or from the opposite strand of reported genomic features. Furthermore, our data revealed the extensive 3' end heterogeneity of yeast genes and identified a novel putative motif for polyadenylation. Our results indicate the yeast transcriptome is more complex than expected. This study would serve as an invaluable resource for elucidating the regulation and evolution of yeast genes.
authors.affiliation: Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors.forename: Ya-Ni
authors.initials: YN
authors.lastname: Kang
authors.forename: Deng-Pan
authors.initials: DP
authors.lastname: Lai
authors.forename: Hong Sain
authors.initials: HS
authors.lastname: Ooi
authors.forename: Ting-Ting
authors.initials: TT
authors.lastname: Shen
authors.forename: Yao
authors.initials: Y
authors.lastname: Kou
authors.forename: Jing
authors.initials: J
authors.lastname: Tian
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Czajkowsky
authors.forename: Zhifeng
authors.initials: Z
authors.lastname: Shao
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Zhao
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D000595:Amino Acid Sequence; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal / Q000235:genetics*; D008969:Molecular Sequence Data; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D024363:Transcription Initiation Site; D059467:Transcriptome / Q000235:genetics*; D020506:Untranslated Regions / Q000235:genetics*
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D012333:RNA, Messenger; D020506:Untranslated Regions