A large-scale full-length cDNA analysis to explore the budding yeast transcriptome

Fumihito Miura, Noriko Kawaguchi, Jun Sese, Atsushi Toyoda, Masahira Hattori, Shinichi Morishita, Takashi Ito

Research output: Contribution to journalArticle

175 Citations (Scopus)

Abstract

We performed a large-scale cDNA analysis to explore the transcriptome of the budding yeast Saccharomyces cerevisiae. We sequenced two cDNA libraries, one from the cells exponentially growing in a minimal medium and the other from meiotic cells. Both libraries were generated by using a vector-capping method that allows the accurate mapping of transcription start sites (TSSs). Consequently, we identified 11,575 TSSs associated with 3,638 annotated genomic features, including 3,599 ORFs, to suggest that most yeast genes have two or more TSSs. In addition, we identified 45 previously undescribed introns, including those affecting current ORF annotations and those spliced alternatively. Furthermore, the analysis revealed 667 transcription units in the intergenic regions and transcripts derived from antisense strands of 367 known features. We also found that 348 ORFs carry TSSs in their 3′-halves to generate sense transcripts starting from inside the ORFs. These results indicate that the budding yeast transcriptome is considerably more complex than previously thought, and it shares many recently revealed characteristics with the transcriptomes of mammals and other higher eukaryotes. Thus, the genome-wide active transcription that generates novel classes of transcripts appears to be an intrinsic feature of the eukaryotic cells. The budding yeast will serve as a versatile model for the studies on these aspects of transcriptome, and the full-length cDNA clones can function as an invaluable resource in such studies.

Original languageEnglish
Pages (from-to)17846-17851
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume103
Issue number47
DOIs
Publication statusPublished - 2006 Nov 21
Externally publishedYes

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Keywords

  • Alternative splicing
  • Antisense transcript
  • Noncoding RNA
  • Transcription start site

ASJC Scopus subject areas

  • Genetics
  • General

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