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

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.

[1]  D. Morris,et al.  Silencing the transcriptome's dark matter: mechanisms for suppressing translation of intergenic transcripts. , 2006, Molecular cell.

[2]  Martin S. Taylor,et al.  Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.

[3]  J. Mattick,et al.  Non-coding RNA. , 2006, Human molecular genetics.

[4]  Wolfgang Huber,et al.  A high-resolution map of transcription in the yeast genome. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Sean R. Collins,et al.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae , 2006, Nature.

[6]  Juan Valcárcel,et al.  The expanding transcriptome: the genome as the ‘Book of Sand’ , 2006, The EMBO journal.

[7]  M. Ares,et al.  Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[8]  P. Walter,et al.  Eisosomes mark static sites of endocytosis , 2006, Nature.

[9]  A. Reymond,et al.  Tandem chimerism as a means to increase protein complexity in the human genome. , 2005, Genome research.

[10]  R. Sorek,et al.  Transcription-mediated gene fusion in the human genome. , 2005, Genome research.

[11]  Kara Dolinski,et al.  Changing perspectives in yeast research nearly a decade after the genome sequence. , 2005, Genome research.

[12]  S. Batalov,et al.  Antisense Transcription in the Mammalian Transcriptome , 2005, Science.

[13]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[14]  F. Dietrich,et al.  Identification and characterization of upstream open reading frames (uORF) in the 5′ untranslated regions (UTR) of genes in Saccharomyces cerevisiae , 2005, Current Genetics.

[15]  B. Séraphin,et al.  Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase , 2005, Cell.

[16]  F. Dietrich,et al.  Mapping of transcription start sites in Saccharomyces cerevisiae using 5′ SAGE , 2005, Nucleic acids research.

[17]  Tomoko Kimura,et al.  Vector-capping: a simple method for preparing a high-quality full-length cDNA library. , 2005, DNA research : an international journal for rapid publication of reports on genes and genomes.

[18]  Gary D Bader,et al.  Global Mapping of the Yeast Genetic Interaction Network , 2004, Science.

[19]  Y. Ishimaru,et al.  Determination of the capped site sequence of mRNA based on the detection of cap-dependent nucleotide addition using an anchor ligation method. , 2004, DNA research : an international journal for rapid publication of reports on genes and genomes.

[20]  Shuyun Dong,et al.  Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast. , 2003, Molecular cell.

[21]  E. O’Shea,et al.  Global analysis of protein expression in yeast , 2003, Nature.

[22]  E. O’Shea,et al.  Global analysis of protein localization in budding yeast , 2003, Nature.

[23]  J. McCarthy,et al.  Regulation of fungal gene expression via short open reading frames in the mRNA 5′untranslated region , 2003, Molecular microbiology.

[24]  L. Fulton,et al.  Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting , 2003, Science.

[25]  B. Birren,et al.  Sequencing and comparison of yeast species to identify genes and regulatory elements , 2003, Nature.

[26]  Kagehiko Kitano,et al.  Automatic Extraction of Expression-Related Features Shared by a Given Group of Genes , 2003 .

[27]  Nicola J. Rinaldi,et al.  Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.

[28]  John R Yates,et al.  Parallel identification of new genes in Saccharomyces cerevisiae. , 2002, Genome research.

[29]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[30]  Satoru Miyano,et al.  Extensive feature detection of N-terminal protein sorting signals , 2002, Bioinform..

[31]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[32]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[33]  Kei-Hoi Cheung,et al.  An integrated approach for finding overlooked genes in yeast , 2002, Nature Biotechnology.

[34]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Yudong D. He,et al.  Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.

[36]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[37]  R Parker,et al.  Analysis of the yeast genome: identification of new non-coding and small ORF-containing RNAs. , 1997, Nucleic acids research.

[38]  V. Iyer,et al.  Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae. , 1996, Proceedings of the National Academy of Sciences of the United States of America.